rs2172487

Positions:

• 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, non coding transcript 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: ENST00000626400.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000626400.1	n.129-3679A>C		intron_variant, non_coding_transcript_variant		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;