rs2172487

Variant names:

• chr11-129608033-A-C
• rs2172487
• ENST00000626400.1:n.129-3679A>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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000626400.1(ENSG00000281386):​n.129-3679A>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 ENST00000626400.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

Genes affected

ENSG00000281386 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000626400.1	n.129-3679A>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

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.744

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2172487; hg19: chr11-129477928;