Variant rs7259 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_016174.5(CERCAM):c.1347G>A(p.Lys449=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,612,898 control chromosomes in the GnomAD database, including 45,610 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.32 ( 10286 hom., cov: 32)

Exomes 𝑓: 0.20 ( 35324 hom. )

Consequence

CERCAM
NM_016174.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.36

Variant links:

Genes affected

CERCAM (HGNC:23723): (cerebral endothelial cell adhesion molecule) Enables identical protein binding activity. Acts upstream of or within cell adhesion. Predicted to be located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Apr 2022]

CERCAM links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP7

Synonymous conserved (PhyloP=1.36 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CERCAM	NM_016174.5 linkuse as main transcript	c.1347G>A	p.Lys449=	synonymous_variant	11/13	ENST00000372838.9
CERCAM	NM_001286760.1 linkuse as main transcript	c.1113G>A	p.Lys371=	synonymous_variant	11/13
CERCAM	XM_011518763.4 linkuse as main transcript	c.1113G>A	p.Lys371=	synonymous_variant	11/13
CERCAM	XM_047423450.1 linkuse as main transcript	c.1113G>A	p.Lys371=	synonymous_variant	12/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CERCAM	ENST00000372838.9 linkuse as main transcript	c.1347G>A	p.Lys449=	synonymous_variant	11/13	1	NM_016174.5	P1	Q5T4B2-1
CERCAM	ENST00000463535.5 linkuse as main transcript	n.1023G>A		non_coding_transcript_exon_variant	8/8	1
CERCAM	ENST00000372842.5 linkuse as main transcript	c.1113G>A	p.Lys371=	synonymous_variant	12/14	5			Q5T4B2-2
CERCAM	ENST00000487001.6 linkuse as main transcript	n.451-1228G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48125

AN:

151774

Hom.:

10258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.265

GnomAD3 exomes

AF:

0.248

AC:

62018

AN:

250386

Hom.:

9183

AF XY:

0.239

AC XY:

32377

AN XY:

135468

show subpopulations

Gnomad AFR exome

AF:

0.622

Gnomad AMR exome

AF:

0.229

Gnomad ASJ exome

AF:

0.146

Gnomad EAS exome

AF:

0.406

Gnomad SAS exome

AF:

0.243

Gnomad FIN exome

AF:

0.243

Gnomad NFE exome

AF:

0.187

Gnomad OTH exome

AF:

0.213

GnomAD4 exome

AF:

0.204

AC:

297917

AN:

1461006

Hom.:

35324

Cov.:

AF XY:

0.204

AC XY:

147987

AN XY:

726866

show subpopulations

Gnomad4 AFR exome

AF:

0.629

Gnomad4 AMR exome

AF:

0.228

Gnomad4 ASJ exome

AF:

0.147

Gnomad4 EAS exome

AF:

0.415

Gnomad4 SAS exome

AF:

0.238

Gnomad4 FIN exome

AF:

0.237

Gnomad4 NFE exome

AF:

0.179

Gnomad4 OTH exome

AF:

0.219

GnomAD4 genome

AF:

0.317

AC:

48208

AN:

151892

Hom.:

10286

Cov.:

AF XY:

0.317

AC XY:

23552

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.613

Gnomad4 AMR

AF:

0.222

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.400

Gnomad4 SAS

AF:

0.251

Gnomad4 FIN

AF:

0.245

Gnomad4 NFE

AF:

0.182

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.228

Hom.:

3695

Bravo

AF:

0.331

Asia WGS

AF:

0.355

AC:

1234

AN:

3478

EpiCase

AF:

0.172

EpiControl

AF:

0.175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

9.6

DANN

Benign

0.44

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over