19-44703663-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_001039213.4(CEACAM16):c.352G>A(p.Glu118Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00273 in 1,576,586 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0022 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 18 hom. )

Consequence

CEACAM16
NM_001039213.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 4.81

Publications

9 publications found

Variant links:

Genes affected

CEACAM16 (HGNC:31948): (CEA cell adhesion molecule 16, tectorial membrane component) The protein encoded by this gene is a secreted glycoprotein that in mouse interacts with tectorial membrane proteins in the inner ear. The encoded adhesion protein is found in cochlear outer hair cells and appears to be important for proper hearing over an extended frequency range. Defects in this gene likely are a cause of non-syndromic autosomal dominant hearing loss. [provided by RefSeq, May 2012]

CEACAM16 links:

CEACAM16-AS1 (HGNC:55317): (CEACAM16, CEACAM19 and PVR antisense RNA 1)

CEACAM16-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 19-44703663-G-A is Benign according to our data. Variant chr19-44703663-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 226506.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00221 (336/152140) while in subpopulation NFE AF = 0.00224 (152/68002). AF 95% confidence interval is 0.00195. There are 2 homozygotes in GnomAd4. There are 145 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 2 AR,AD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039213.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM16	NM_001039213.4	MANE Select	c.352G>A	p.Glu118Lys	missense	Exon 3 of 7	NP_001034302.2	Q2WEN9
	CEACAM16-AS1	NR_186815.1		n.348-4486C>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CEACAM16	ENST00000587331.7	TSL:1 MANE Select	c.352G>A	p.Glu118Lys	missense	Exon 3 of 7	ENSP00000466561.1	Q2WEN9
CEACAM16	ENST00000405314.2	TSL:5	c.352G>A	p.Glu118Lys	missense	Exon 2 of 6	ENSP00000385576.1	Q2WEN9
CEACAM16-AS1	ENST00000590796.1	TSL:5	n.315-4486C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00221

AC:

336

AN:

152022

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000556

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00209

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00223

Gnomad OTH

AF:

0.00670

GnomAD2 exomes

AF:

0.00329

AC:

676

AN:

205396

AF XY:

0.00326

show subpopulations

Gnomad AFR exome

AF:

0.000557

Gnomad AMR exome

AF:

0.00244

Gnomad ASJ exome

AF:

0.0385

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000533

Gnomad NFE exome

AF:

0.00244

Gnomad OTH exome

AF:

0.00480

GnomAD4 exome

AF:

0.00279

AC:

3972

AN:

1424446

Hom.:

Cov.:

AF XY:

0.00286

AC XY:

2015

AN XY:

703432

show subpopulations

African (AFR)

AF:

0.000304

AC:

AN:

32888

American (AMR)

AF:

0.00238

AC:

100

AN:

41934

Ashkenazi Jewish (ASJ)

AF:

0.0354

AC:

856

AN:

24206

East Asian (EAS)

AF:

0.00

AC:

AN:

38744

South Asian (SAS)

AF:

0.00233

AC:

189

AN:

80978

European-Finnish (FIN)

AF:

0.0000588

AC:

AN:

51042

Middle Eastern (MID)

AF:

0.00177

AC:

AN:

5664

European-Non Finnish (NFE)

AF:

0.00233

AC:

2537

AN:

1090158

Other (OTH)

AF:

0.00454

AC:

267

AN:

58832

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

222

444

666

888

1110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

220

330

440

550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00221

AC:

336

AN:

152140

Hom.:

Cov.:

AF XY:

0.00195

AC XY:

145

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.000554

AC:

AN:

41498

American (AMR)

AF:

0.00209

AC:

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0323

AC:

112

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5154

South Asian (SAS)

AF:

0.000622

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10580

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00224

AC:

152

AN:

68002

Other (OTH)

AF:

0.00663

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00305

Hom.:

Bravo

AF:

0.00296

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00104

AC:

ESP6500AA

AF:

0.000964

AC:

ESP6500EA

AF:

0.00274

AC:

ExAC

AF:

0.00244

AC:

294

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (4)

not specified (3)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.25

CADD

Pathogenic

(source)

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.067

Eigen

Uncertain

0.42

Eigen_PC

Uncertain

0.41

FATHMM_MKL

Uncertain

0.91

LIST_S2

Benign

0.86

M_CAP

Benign

0.071

MetaRNN

Benign

0.0084

MetaSVM

Uncertain

-0.27

MutationAssessor

Benign

2.0

PhyloP100

4.8

PrimateAI

Uncertain

0.53

PROVEAN

Uncertain

-2.4

REVEL

Benign

0.20

Sift

Benign

0.047

Sift4G

Uncertain

0.060

Vest4

0.61

MVP

0.77

MPC

0.53

ClinPred

0.032

GERP RS

5.2

Varity_R

0.22

gMVP

0.56

Mutation Taster

=98/2

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.32

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.32

Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over