rs11088859

Variant names:

• chr21-21317024-G-A
• rs11088859
• NM_004540.5:c.620-7359G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-21317024-G-A
• chr21-21317024-G-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.620-7359G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0459 in 152,092 control chromosomes in the GnomAD database, including 293 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 0.046 (293 hom., cov: 32)
• Consequence: NCAM2 NM_004540.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCAM2	NM_004540.5	MANE Select	c.620-7359G>A		intron	N/A	NP_004531.2
	NCAM2	NM_001352592.2		c.695-7359G>A		intron	N/A	NP_001339521.1
	NCAM2	NM_001352591.2		c.620-7359G>A		intron	N/A	NP_001339520.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCAM2	ENST00000400546.6	TSL:1 MANE Select	c.620-7359G>A		intron	N/A	ENSP00000383392.1	O15394-1
	NCAM2	ENST00000284894.8	TSL:5	c.566-7359G>A		intron	N/A	ENSP00000284894.8	H9KV31
	NCAM2	ENST00000461281.1	TSL:3	n.214-7359G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 6982 AN: 151974 Hom.: 292 Cov.: 32

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0331

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

GnomAD4 genome AF: 0.0459 AC: 6985 AN: 152092 Hom.: 293 Cov.: 32 AF XY: 0.0471 AC XY: 3502 AN XY: 74344

African (AFR) AF: 0.0834 AC: 3460 AN: 41488

American (AMR) AF: 0.0511 AC: 781 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3466

East Asian (EAS) AF: 0.191 AC: 987 AN: 5162

South Asian (SAS) AF: 0.0324 AC: 156 AN: 4822

European-Finnish (FIN) AF: 0.0374 AC: 395 AN: 10564

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0165 AC: 1119 AN: 67992

Other (OTH) AF: 0.0332 AC: 70 AN: 2108

Alfa AF: 0.0264 Hom.: 478

Bravo AF: 0.0487

Asia WGS AF: 0.107 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		-0.0060
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: rs11088859; hg19: chr21-22689344;