rs232378

Variant names:

• chr21-21348119-T-A
• rs232378
• NM_004540.5:c.1044+9585T>A

Your query was ambiguous. Multiple possible variants found:

• chr21-21348119-T-A
• chr21-21348119-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004540.5(NCAM2):​c.1044+9585T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,764 control chromosomes in the GnomAD database, including 14,458 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 0.43 (14458 hom., cov: 32)
• Consequence: NCAM2 NM_004540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCAM2	NM_004540.5	c.1044+9585T>A		intron_variant	Intron 8 of 17	ENST00000400546.6	NP_004531.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCAM2	ENST00000400546.6	c.1044+9585T>A		intron_variant	Intron 8 of 17	1	NM_004540.5	ENSP00000383392.1
NCAM2	ENST00000284894.8	c.990+9585T>A		intron_variant	Intron 7 of 16	5		ENSP00000284894.8

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65735 AN: 151650 Hom.: 14453 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.433 AC: 65779 AN: 151764 Hom.: 14458 Cov.: 32 AF XY: 0.431 AC XY: 31955 AN XY: 74134

African (AFR) AF: 0.384 AC: 15908 AN: 41418

American (AMR) AF: 0.351 AC: 5351 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1807 AN: 3468

East Asian (EAS) AF: 0.586 AC: 3015 AN: 5146

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4816

European-Finnish (FIN) AF: 0.434 AC: 4571 AN: 10538

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31606 AN: 67814

Other (OTH) AF: 0.427 AC: 897 AN: 2102

Alfa AF: 0.458 Hom.: 1986

Bravo AF: 0.428

Asia WGS AF: 0.470 AC: 1635 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.16
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs232378; hg19: chr21-22720439;