8-5017650-G-T

Position:

• chr8-5017650-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.652 in 152,070 control chromosomes in the GnomAD database, including 32,928 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 0.65 (32928 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99133 AN: 151952 Hom.: 32896 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.675

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.652 AC: 99216 AN: 152070 Hom.: 32928 Cov.: 32 AF XY: 0.646 AC XY: 47995 AN XY: 74328

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.674

Alfa AF: 0.643 Hom.: 53215

Bravo AF: 0.653

Asia WGS AF: 0.655 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.031
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10112481; hg19: chr8-4875172;