chr8-31176759-C-T

Variant names:

• chr8-31176759-C-T
• rs11774682
• ENST00000521252.1:n.114G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000521252.1(ENSG00000253961):​n.114G>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 0.0263 in 152,208 control chromosomes in the GnomAD database, including 73 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 0.026 (72 hom., cov: 32)
  • Exomes 𝑓: 0.11 (1 hom.)
• Consequence: ENSG00000253961 ENST00000521252.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 2 publications found

Genes affected

ENSG00000253961 (HGNC:58431):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0263 (3999/152190) while in subpopulation NFE AF = 0.0419 (2851/68006). AF 95% confidence interval is 0.0406. There are 72 homozygotes in GnomAd4. There are 1831 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 72 gene

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
ENSG00000253961	ENST00000521252.1	n.114G>A		non_coding_transcript_exon_variant	Exon 1 of 2	5
ENSG00000253961	ENST00000523365.1	n.321G>A		non_coding_transcript_exon_variant	Exon 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0263 AC: 4003 AN: 152072 Hom.: 72 Cov.: 32

Gnomad AFR AF: 0.00824

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.00821

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0420

Gnomad OTH AF: 0.0344

GnomAD4 exome AF: 0.111 AC: 2 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.125 AC XY: 2 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.167 AC: 2 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0263 AC: 3999 AN: 152190 Hom.: 72 Cov.: 32 AF XY: 0.0246 AC XY: 1831 AN XY: 74400

African (AFR) AF: 0.00821 AC: 341 AN: 41510

American (AMR) AF: 0.0319 AC: 488 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0182 AC: 63 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00435 AC: 21 AN: 4826

European-Finnish (FIN) AF: 0.00821 AC: 87 AN: 10594

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0419 AC: 2851 AN: 68006

Other (OTH) AF: 0.0341 AC: 72 AN: 2114

Alfa AF: 0.0354 Hom.: 145

Bravo AF: 0.0279

Asia WGS AF: 0.00289 AC: 10 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	5.8
DANN	Benign	0.73
PhyloP100		-0.075
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11774682; hg19: chr8-31034275;