rs12909691

Variant names:

• chr15-93301533-C-T
• rs12909691
• ENST00000556538.1:n.115G>A

Variant summary

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

The ENST00000556538.1(ENSG00000258971):​n.115G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 520,300 control chromosomes in the GnomAD database, including 120,007 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 0.62 (31401 hom., cov: 33)
  • Exomes 𝑓: 0.68 (88606 hom.)
• Consequence: ENSG00000258971 ENST00000556538.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 5 publications found

Genes affected

ENSG00000258971 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370982	XR_007064770.1	n.1160+42296C>T		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258971	ENST00000556538.1	n.115G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000257060	ENST00000667030.1	n.236+42296C>T		intron_variant	Intron 2 of 8
ENSG00000257060	ENST00000791023.1	n.533+69681C>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94774 AN: 151948 Hom.: 31407 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.672

GnomAD2 exomes AF: 0.643 AC: 151746 AN: 236076 AF XY: 0.659

Gnomad AFR exome AF: 0.422

Gnomad AMR exome AF: 0.552

Gnomad ASJ exome AF: 0.715

Gnomad EAS exome AF: 0.223

Gnomad FIN exome AF: 0.710

Gnomad NFE exome AF: 0.740

Gnomad OTH exome AF: 0.675

GnomAD4 exome AF: 0.682 AC: 251221 AN: 368232 Hom.: 88606 Cov.: 0 AF XY: 0.689 AC XY: 145292 AN XY: 210856

African (AFR) AF: 0.437 AC: 4555 AN: 10420

American (AMR) AF: 0.554 AC: 19763 AN: 35650

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 8418 AN: 11652

East Asian (EAS) AF: 0.228 AC: 3008 AN: 13182

South Asian (SAS) AF: 0.691 AC: 46364 AN: 67116

European-Finnish (FIN) AF: 0.715 AC: 14741 AN: 20622

Middle Eastern (MID) AF: 0.676 AC: 1922 AN: 2842

European-Non Finnish (NFE) AF: 0.742 AC: 141106 AN: 190232

Other (OTH) AF: 0.687 AC: 11344 AN: 16516

GnomAD4 genome AF: 0.623 AC: 94787 AN: 152068 Hom.: 31401 Cov.: 33 AF XY: 0.622 AC XY: 46217 AN XY: 74322

African (AFR) AF: 0.431 AC: 17869 AN: 41460

American (AMR) AF: 0.617 AC: 9422 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2520 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1203 AN: 5174

South Asian (SAS) AF: 0.681 AC: 3285 AN: 4822

European-Finnish (FIN) AF: 0.726 AC: 7678 AN: 10576

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.743 AC: 50533 AN: 67976

Other (OTH) AF: 0.672 AC: 1416 AN: 2108

Alfa AF: 0.697 Hom.: 16721

Bravo AF: 0.603

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12909691; hg19: chr15-93844762;