dbSNP rs146757817: CEACAM16:p.Ter426Ter (chr19-44710506-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001039213.4(CEACAM16):c.1278A>G(p.Ter426Ter) variant causes a stop retained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.016 in 1,613,546 control chromosomes in the GnomAD database, including 253 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 17 hom., cov: 33)

Exomes 𝑓: 0.016 ( 236 hom. )

Consequence

CEACAM16
NM_001039213.4 stop_retained

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 1.56

Publications

2 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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 19-44710506-A-G is Benign according to our data. Variant chr19-44710506-A-G is described in ClinVar as Benign. ClinVar VariationId is 226505.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.56 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.012 (1826/152270) while in subpopulation NFE AF = 0.017 (1159/68006). AF 95% confidence interval is 0.0162. There are 17 homozygotes in GnomAd4. There are 864 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 17 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.1278A>G	p.Ter426Ter	stop_retained	Exon 7 of 7	NP_001034302.2	Q2WEN9
	CEACAM16-AS1	NR_186815.1		n.348-11329T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CEACAM16	ENST00000587331.7	TSL:1 MANE Select	c.1278A>G	p.Ter426Ter	stop_retained	Exon 7 of 7	ENSP00000466561.1	Q2WEN9
CEACAM16	ENST00000405314.2	TSL:5	c.1278A>G	p.Ter426Ter	stop_retained	Exon 6 of 6	ENSP00000385576.1	Q2WEN9
CEACAM16-AS1	ENST00000590796.1	TSL:5	n.314+5444T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0120

AC:

1828

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00352

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0166

Gnomad ASJ

AF:

0.0231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0124

Gnomad FIN

AF:

0.00819

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0170

Gnomad OTH

AF:

0.0158

GnomAD2 exomes

AF:

0.0143

AC:

3553

AN:

248868

AF XY:

0.0145

show subpopulations

Gnomad AFR exome

AF:

0.00239

Gnomad AMR exome

AF:

0.0115

Gnomad ASJ exome

AF:

0.0212

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00965

Gnomad NFE exome

AF:

0.0194

Gnomad OTH exome

AF:

0.0212

GnomAD4 exome

AF:

0.0164

AC:

23922

AN:

1461276

Hom.:

236

Cov.:

AF XY:

0.0162

AC XY:

11764

AN XY:

726960

show subpopulations

African (AFR)

AF:

0.00269

AC:

AN:

33476

American (AMR)

AF:

0.0109

AC:

486

AN:

44704

Ashkenazi Jewish (ASJ)

AF:

0.0210

AC:

549

AN:

26106

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39690

South Asian (SAS)

AF:

0.0120

AC:

1037

AN:

86238

European-Finnish (FIN)

AF:

0.00995

AC:

531

AN:

53384

Middle Eastern (MID)

AF:

0.0266

AC:

153

AN:

5762

European-Non Finnish (NFE)

AF:

0.0181

AC:

20098

AN:

1111568

Other (OTH)

AF:

0.0162

AC:

977

AN:

60348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

1160

2321

3481

4642

5802

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

752

1504

2256

3008

3760

<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:

0.0120

AC:

1826

AN:

152270

Hom.:

Cov.:

AF XY:

0.0116

AC XY:

864

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.00351

AC:

146

AN:

41552

American (AMR)

AF:

0.0165

AC:

253

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0231

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5172

South Asian (SAS)

AF:

0.0126

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00819

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0170

AC:

1159

AN:

68006

Other (OTH)

AF:

0.0156

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

192

288

384

480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.0135

Hom.:

Bravo

AF:

0.0120

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.0187

EpiControl

AF:

0.0186

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (4)

not specified (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.7

(source)

DANN

Benign

0.61

PhyloP100

1.6

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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