rs10932886

Variant names:

• chr2-220855368-G-A
• rs10932886
• ENST00000651076.2:n.359-1686C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-220855368-G-A
• chr2-220855368-G-T

Variant summary

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

The ENST00000651076.2(ENSG00000286272):​n.359-1686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,040 control chromosomes in the GnomAD database, including 6,652 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 0.29 (6652 hom., cov: 32)
• Consequence: ENSG00000286272 ENST00000651076.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 15 publications found

Genes affected

ENSG00000286272 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985990	XR_001739902.1	n.276-367G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286272	ENST00000651076.2	n.359-1686C>T		intron_variant	Intron 1 of 2
ENSG00000288902	ENST00000658049.1	n.660-367G>A		intron_variant	Intron 6 of 6
ENSG00000286272	ENST00000830583.1	n.370-1686C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43958 AN: 151920 Hom.: 6655 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.289 AC: 43965 AN: 152040 Hom.: 6652 Cov.: 32 AF XY: 0.280 AC XY: 20814 AN XY: 74316

African (AFR) AF: 0.235 AC: 9754 AN: 41470

American (AMR) AF: 0.289 AC: 4409 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3468

East Asian (EAS) AF: 0.171 AC: 887 AN: 5174

South Asian (SAS) AF: 0.204 AC: 984 AN: 4814

European-Finnish (FIN) AF: 0.247 AC: 2607 AN: 10568

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23169 AN: 67970

Other (OTH) AF: 0.312 AC: 657 AN: 2108

Alfa AF: 0.312 Hom.: 18942

Bravo AF: 0.288

Asia WGS AF: 0.210 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.014
DANN	Benign	0.36
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10932886; hg19: chr2-221720088;