dbSNP rs10426475: CEACAM16:c.941-14C>T (chr19-44707847-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001039213.4(CEACAM16):c.941-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0418 in 1,514,672 control chromosomes in the GnomAD database, including 2,023 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 393 hom., cov: 32)

Exomes 𝑓: 0.040 ( 1630 hom. )

Consequence

CEACAM16
NM_001039213.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.207

Publications

1 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 -20 ACMG points.

BP4

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

BP6

Variant 19-44707847-C-T is Benign according to our data. Variant chr19-44707847-C-T is described in ClinVar as Benign. ClinVar VariationId is 226510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

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.941-14C>T		intron	N/A	NP_001034302.2	Q2WEN9
	CEACAM16-AS1	NR_186815.1		n.348-8670G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CEACAM16	ENST00000587331.7	TSL:1 MANE Select	c.941-14C>T	intron	N/A	ENSP00000466561.1	Q2WEN9
CEACAM16	ENST00000405314.2	TSL:5	c.941-14C>T	intron	N/A	ENSP00000385576.1	Q2WEN9
CEACAM16-AS1	ENST00000590796.1	TSL:5	n.314+8103G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0595

AC:

9057

AN:

152106

Hom.:

391

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0865

Gnomad AMI

AF:

0.0253

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.0308

Gnomad EAS

AF:

0.0512

Gnomad SAS

AF:

0.0811

Gnomad FIN

AF:

0.0451

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0311

Gnomad OTH

AF:

0.0630

GnomAD2 exomes

AF:

0.0636

AC:

10971

AN:

172482

AF XY:

0.0598

show subpopulations

Gnomad AFR exome

AF:

0.0891

Gnomad AMR exome

AF:

0.177

Gnomad ASJ exome

AF:

0.0263

Gnomad EAS exome

AF:

0.0419

Gnomad FIN exome

AF:

0.0516

Gnomad NFE exome

AF:

0.0312

Gnomad OTH exome

AF:

0.0510

GnomAD4 exome

AF:

0.0399

AC:

54319

AN:

1362448

Hom.:

1630

Cov.:

AF XY:

0.0402

AC XY:

26763

AN XY:

665002

show subpopulations

African (AFR)

AF:

0.0877

AC:

2742

AN:

31264

American (AMR)

AF:

0.170

AC:

5993

AN:

35250

Ashkenazi Jewish (ASJ)

AF:

0.0272

AC:

572

AN:

21038

East Asian (EAS)

AF:

0.0486

AC:

1820

AN:

37446

South Asian (SAS)

AF:

0.0745

AC:

5280

AN:

70896

European-Finnish (FIN)

AF:

0.0496

AC:

2414

AN:

48692

Middle Eastern (MID)

AF:

0.0374

AC:

175

AN:

4674

European-Non Finnish (NFE)

AF:

0.0310

AC:

32807

AN:

1057142

Other (OTH)

AF:

0.0449

AC:

2516

AN:

56046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

2791

5582

8372

11163

13954

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1442

2884

4326

5768

7210

<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:

0.0595

AC:

9061

AN:

152224

Hom.:

393

Cov.:

AF XY:

0.0622

AC XY:

4626

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.0863

AC:

3584

AN:

41530

American (AMR)

AF:

0.128

AC:

1962

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0308

AC:

107

AN:

3470

East Asian (EAS)

AF:

0.0510

AC:

264

AN:

5180

South Asian (SAS)

AF:

0.0805

AC:

389

AN:

4832

European-Finnish (FIN)

AF:

0.0451

AC:

478

AN:

10596

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0311

AC:

2115

AN:

68016

Other (OTH)

AF:

0.0619

AC:

131

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

439

877

1316

1754

2193

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<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:

0.0432

Hom.:

376

Bravo

AF:

0.0680

Asia WGS

AF:

0.0720

AC:

251

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

not specified (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.78

(source)

DANN

Benign

0.40

PhyloP100

-0.21

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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