rs11774682

Positions:

• chr8-31176759-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000521252.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 72 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000521252.1	n.114G>A		non_coding_transcript_exon_variant	1/2	5
	ENST00000523365.1	n.321G>A		non_coding_transcript_exon_variant	2/4	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

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

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

Gnomad4 AFR AF: 0.00821

Gnomad4 AMR AF: 0.0319

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00435

Gnomad4 FIN AF: 0.00821

Gnomad4 NFE AF: 0.0419

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0312 Hom.: 11

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11774682; hg19: chr8-31034275;