NM_004540.5:c.55+139818A>G

Variant names:

• chr21-21138436-A-G
• rs2826689
• NM_004540.5:c.55+139818A>G

Variant summary

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

The NM_004540.5(NCAM2):​c.55+139818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,592 control chromosomes in the GnomAD database, including 9,936 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 0.36 (9936 hom., cov: 32)
• Consequence: NCAM2 NM_004540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004540.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCAM2	NM_004540.5	MANE Select	c.55+139818A>G		intron	N/A	NP_004531.2
	NCAM2	NM_001352592.2		c.-21-72105A>G		intron	N/A	NP_001339521.1
	NCAM2	NM_001352591.2		c.55+139818A>G		intron	N/A	NP_001339520.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCAM2	ENST00000400546.6	TSL:1 MANE Select	c.55+139818A>G		intron	N/A	ENSP00000383392.1

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54859 AN: 151474 Hom.: 9932 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.362 AC: 54899 AN: 151592 Hom.: 9936 Cov.: 32 AF XY: 0.357 AC XY: 26422 AN XY: 74060

African (AFR) AF: 0.354 AC: 14597 AN: 41274

American (AMR) AF: 0.331 AC: 5031 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3466

East Asian (EAS) AF: 0.417 AC: 2133 AN: 5120

South Asian (SAS) AF: 0.330 AC: 1581 AN: 4794

European-Finnish (FIN) AF: 0.347 AC: 3651 AN: 10512

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.374 AC: 25418 AN: 67936

Other (OTH) AF: 0.357 AC: 750 AN: 2098

Alfa AF: 0.368 Hom.: 1474

Bravo AF: 0.363

Asia WGS AF: 0.372 AC: 1289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.31
PhyloP100		0.20
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: rs2826689; hg19: chr21-22510754;