Variant chr7-108232372-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001037132.4(NRCAM):c.381C>T(p.Asn127=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,609,834 control chromosomes in the GnomAD database, including 25,042 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 0.14 ( 2362 hom., cov: 32)

Exomes 𝑓: 0.15 ( 22680 hom. )

Consequence

NRCAM
NM_001037132.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.651

Variant links:

Genes affected

NRCAM (HGNC:7994): (neuronal cell adhesion molecule) Cell adhesion molecules (CAMs) are members of the immunoglobulin superfamily. This gene encodes a neuronal cell adhesion molecule with multiple immunoglobulin-like C2-type domains and fibronectin type-III domains. This ankyrin-binding protein is involved in neuron-neuron adhesion and promotes directional signaling during axonal cone growth. This gene is also expressed in non-neural tissues and may play a general role in cell-cell communication via signaling from its intracellular domain to the actin cytoskeleton during directional cell migration. Allelic variants of this gene have been associated with autism and addiction vulnerability. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

NRCAM links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP7

Synonymous conserved (PhyloP=-0.651 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRCAM	NM_001037132.4 linkuse as main transcript	c.381C>T	p.Asn127=	synonymous_variant	7/33	ENST00000379028.8	NP_001032209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NRCAM	ENST00000379028.8 linkuse as main transcript	c.381C>T	p.Asn127=	synonymous_variant	7/33	5	NM_001037132.4	ENSP00000368314	P1	Q92823-1

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20714

AN:

151990

Hom.:

2361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0286

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.560

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.153

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.136

Gnomad OTH

AF:

0.137

GnomAD3 exomes

AF:

0.205

AC:

50713

AN:

246956

Hom.:

7790

AF XY:

0.202

AC XY:

26924

AN XY:

133474

show subpopulations

Gnomad AFR exome

AF:

0.0259

Gnomad AMR exome

AF:

0.364

Gnomad ASJ exome

AF:

0.110

Gnomad EAS exome

AF:

0.578

Gnomad SAS exome

AF:

0.226

Gnomad FIN exome

AF:

0.155

Gnomad NFE exome

AF:

0.138

Gnomad OTH exome

AF:

0.173

GnomAD4 exome

AF:

0.154

AC:

224038

AN:

1457726

Hom.:

22680

Cov.:

AF XY:

0.156

AC XY:

113080

AN XY:

725132

show subpopulations

Gnomad4 AFR exome

AF:

0.0208

Gnomad4 AMR exome

AF:

0.347

Gnomad4 ASJ exome

AF:

0.112

Gnomad4 EAS exome

AF:

0.545

Gnomad4 SAS exome

AF:

0.231

Gnomad4 FIN exome

AF:

0.157

Gnomad4 NFE exome

AF:

0.131

Gnomad4 OTH exome

AF:

0.153

GnomAD4 genome

AF:

0.136

AC:

20716

AN:

152108

Hom.:

2362

Cov.:

AF XY:

0.143

AC XY:

10622

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.0286

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.561

Gnomad4 SAS

AF:

0.219

Gnomad4 FIN

AF:

0.153

Gnomad4 NFE

AF:

0.136

Gnomad4 OTH

AF:

0.134

Alfa

AF:

0.141

Hom.:

3052

Bravo

AF:

0.141

Asia WGS

AF:

0.295

AC:

1024

AN:

3478

EpiCase

AF:

0.141

EpiControl

AF:

0.139

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

0.15

DANN

Benign

0.73

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

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