rs2155798

chr21-21176833-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004540.5(NCAM2):c.56-103745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 151,562 control chromosomes in the GnomAD database, including 51,595 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 0.80 (51595 hom., cov: 30)
• Consequence: NCAM2 NM_004540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

Genes affected

NCAM2 (HGNC:7657): (neural cell adhesion molecule 2) The protein encoded by this gene belongs to the immunoglobulin superfamily. It is a type I membrane protein and may function in selective fasciculation and zone-to-zone projection of the primary olfactory axons. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCAM2	NM_004540.5	c.56-103745A>G		intron_variant		ENST00000400546.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCAM2	ENST00000400546.6	c.56-103745A>G		intron_variant		1	NM_004540.5	P1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121264 AN: 151442 Hom.: 51593 Cov.: 30

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.862

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.830

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.800 AC: 121301 AN: 151562 Hom.: 51595 Cov.: 30 AF XY: 0.799 AC XY: 59176 AN XY: 74046

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.826

Alfa AF: 0.878 Hom.: 13101

Bravo AF: 0.778

Asia WGS AF: 0.661 AC: 2273 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.3
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

Other links and lift over

dbSNP: rs2155798; hg19: chr21-22549151;