rs2172487

Variant names:

• chr11-129608033-A-C
• rs2172487
• ENST00000626400.2:n.131-3679A>C

Your query was ambiguous. Multiple possible variants found:

• chr11-129608033-A-C
• chr11-129608033-A-G
• chr11-129608033-A-T

Variant summary

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

The ENST00000626400.2(ENSG00000281386):​n.131-3679A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,724 control chromosomes in the GnomAD database, including 39,005 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 0.71 (39005 hom., cov: 29)
• Consequence: ENSG00000281386 ENST00000626400.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 2 publications found

Genes affected

ENSG00000281386 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000281386	ENST00000626400.2	n.131-3679A>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108194 AN: 151606 Hom.: 38979 Cov.: 29

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.714 AC: 108274 AN: 151724 Hom.: 39005 Cov.: 29 AF XY: 0.712 AC XY: 52806 AN XY: 74148

African (AFR) AF: 0.624 AC: 25760 AN: 41310

American (AMR) AF: 0.764 AC: 11642 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2830 AN: 3468

East Asian (EAS) AF: 0.770 AC: 3984 AN: 5174

South Asian (SAS) AF: 0.809 AC: 3885 AN: 4800

European-Finnish (FIN) AF: 0.639 AC: 6710 AN: 10498

Middle Eastern (MID) AF: 0.836 AC: 244 AN: 292

European-Non Finnish (NFE) AF: 0.752 AC: 51091 AN: 67930

Other (OTH) AF: 0.744 AC: 1568 AN: 2108

Alfa AF: 0.691 Hom.: 3246

Bravo AF: 0.719

Asia WGS AF: 0.796 AC: 2766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.74
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2172487; hg19: chr11-129477928;