dbSNP rs62120572: CEACAM16:c.1268-16C>T (chr19-44710480-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.1268-16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 1,611,444 control chromosomes in the GnomAD database, including 1,854 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 169 hom., cov: 33)

Exomes 𝑓: 0.046 ( 1685 hom. )

Consequence

CEACAM16
NM_001039213.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.02

Publications

4 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=-0.8).

BP6

Variant 19-44710480-C-T is Benign according to our data. Variant chr19-44710480-C-T is described in ClinVar as Benign. ClinVar VariationId is 257226.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0603 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.1268-16C>T		intron	N/A	NP_001034302.2	Q2WEN9
	CEACAM16-AS1	NR_186815.1		n.348-11303G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CEACAM16	ENST00000587331.7	TSL:1 MANE Select	c.1268-16C>T	intron	N/A	ENSP00000466561.1	Q2WEN9
CEACAM16	ENST00000405314.2	TSL:5	c.1268-16C>T	intron	N/A	ENSP00000385576.1	Q2WEN9
CEACAM16-AS1	ENST00000590796.1	TSL:5	n.314+5470G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0418

AC:

6357

AN:

152130

Hom.:

169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0341

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.0284

Gnomad ASJ

AF:

0.0357

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0666

Gnomad FIN

AF:

0.0414

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0501

Gnomad OTH

AF:

0.0449

GnomAD2 exomes

AF:

0.0428

AC:

10575

AN:

247160

AF XY:

0.0458

show subpopulations

Gnomad AFR exome

AF:

0.0343

Gnomad AMR exome

AF:

0.0190

Gnomad ASJ exome

AF:

0.0321

Gnomad EAS exome

AF:

0.000393

Gnomad FIN exome

AF:

0.0438

Gnomad NFE exome

AF:

0.0514

Gnomad OTH exome

AF:

0.0438

GnomAD4 exome

AF:

0.0461

AC:

67297

AN:

1459196

Hom.:

1685

Cov.:

AF XY:

0.0474

AC XY:

34378

AN XY:

725754

show subpopulations

African (AFR)

AF:

0.0377

AC:

1260

AN:

33418

American (AMR)

AF:

0.0209

AC:

930

AN:

44592

Ashkenazi Jewish (ASJ)

AF:

0.0321

AC:

837

AN:

26050

East Asian (EAS)

AF:

0.000253

AC:

AN:

39556

South Asian (SAS)

AF:

0.0701

AC:

6031

AN:

86014

European-Finnish (FIN)

AF:

0.0471

AC:

2513

AN:

53352

Middle Eastern (MID)

AF:

0.0546

AC:

314

AN:

5750

European-Non Finnish (NFE)

AF:

0.0477

AC:

52946

AN:

1110222

Other (OTH)

AF:

0.0408

AC:

2456

AN:

60242

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

3332

6665

9997

13330

16662

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1952

3904

5856

7808

9760

<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:

0.0418

AC:

6359

AN:

152248

Hom.:

169

Cov.:

AF XY:

0.0420

AC XY:

3126

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0341

AC:

1416

AN:

41526

American (AMR)

AF:

0.0284

AC:

434

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0357

AC:

124

AN:

3472

East Asian (EAS)

AF:

0.000579

AC:

AN:

5182

South Asian (SAS)

AF:

0.0663

AC:

320

AN:

4830

European-Finnish (FIN)

AF:

0.0414

AC:

439

AN:

10616

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0502

AC:

3410

AN:

67996

Other (OTH)

AF:

0.0449

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

302

604

905

1207

1509

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<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:

0.0464

Hom.:

Bravo

AF:

0.0385

Asia WGS

AF:

0.0310

AC:

107

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 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

1.0

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