8-116339735-G-T

Variant names:

• chr8-116339735-G-T
• rs2316692

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 0.152 in 151,736 control chromosomes in the GnomAD database, including 2,164 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 0.15 (2164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

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

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23051 AN: 151634 Hom.: 2148 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.152 AC: 23108 AN: 151736 Hom.: 2164 Cov.: 32 AF XY: 0.153 AC XY: 11356 AN XY: 74142

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0816

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.139

Alfa AF: 0.109 Hom.: 1528

Bravo AF: 0.155

Asia WGS AF: 0.122 AC: 425 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	0.038
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2316692; hg19: chr8-117351973;