chr7-108422794-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001037132.4(NRCAM):​c.-331-23201A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,950 control chromosomes in the GnomAD database, including 18,485 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 0.49 ( 18485 hom., cov: 32)

Consequence

NRCAM
NM_001037132.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.878
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NRCAMNM_001037132.4 linkuse as main transcriptc.-331-23201A>G intron_variant ENST00000379028.8 NP_001032209.1 Q92823-1Q14CA1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NRCAMENST00000379028.8 linkuse as main transcriptc.-331-23201A>G intron_variant 5 NM_001037132.4 ENSP00000368314.3 Q92823-1

Frequencies

GnomAD3 genomes
AF:
0.492
AC:
74671
AN:
151830
Hom.:
18464
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.523
Gnomad AMI
AF:
0.438
Gnomad AMR
AF:
0.457
Gnomad ASJ
AF:
0.422
Gnomad EAS
AF:
0.397
Gnomad SAS
AF:
0.480
Gnomad FIN
AF:
0.504
Gnomad MID
AF:
0.337
Gnomad NFE
AF:
0.493
Gnomad OTH
AF:
0.448
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.492
AC:
74734
AN:
151950
Hom.:
18485
Cov.:
32
AF XY:
0.490
AC XY:
36395
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.523
Gnomad4 AMR
AF:
0.458
Gnomad4 ASJ
AF:
0.422
Gnomad4 EAS
AF:
0.396
Gnomad4 SAS
AF:
0.479
Gnomad4 FIN
AF:
0.504
Gnomad4 NFE
AF:
0.493
Gnomad4 OTH
AF:
0.442
Alfa
AF:
0.481
Hom.:
23645
Bravo
AF:
0.486
Asia WGS
AF:
0.386
AC:
1344
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.83
DANN
Benign
0.44

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.

Other links and lift over

dbSNP: rs2300045; hg19: chr7-108063238; API