rs12909691

chr15-93301533-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000556538.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105370982	XR_007064770.1	n.1160+42296C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000556538.1	n.115G>A		non_coding_transcript_exon_variant	1/1
	ENST00000667030.1	n.236+42296C>T		intron_variant, non_coding_transcript_variant

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

GnomAD3 exomes AF: 0.643 AC: 151746 AN: 236076 Hom.: 51720 AF XY: 0.659 AC XY: 84737 AN XY: 128656

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 SAS exome AF: 0.692

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

Gnomad4 AFR exome AF: 0.437

Gnomad4 AMR exome AF: 0.554

Gnomad4 ASJ exome AF: 0.722

Gnomad4 EAS exome AF: 0.228

Gnomad4 SAS exome AF: 0.691

Gnomad4 FIN exome AF: 0.715

Gnomad4 NFE exome AF: 0.742

Gnomad4 OTH exome AF: 0.687

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

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.672

Alfa AF: 0.694 Hom.: 11399

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12909691; hg19: chr15-93844762;