rs6983039

Variant names:

• chr8-115318626-G-A
• rs6983039

Your query was ambiguous. Multiple possible variants found:

• chr8-115318626-G-A
• chr8-115318626-G-C
• chr8-115318626-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 0.101 in 150,486 control chromosomes in the GnomAD database, including 1,141 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 0.10 (1141 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 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: 0.101 AC: 15198 AN: 150438 Hom.: 1149 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.0871

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.101 AC: 15208 AN: 150486 Hom.: 1141 Cov.: 31 AF XY: 0.102 AC XY: 7516 AN XY: 73342

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0629

Gnomad4 EAS AF: 0.0524

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0557

Gnomad4 NFE AF: 0.0450

Gnomad4 OTH AF: 0.0889

Alfa AF: 0.0682 Hom.: 92

Bravo AF: 0.105

Asia WGS AF: 0.107 AC: 370 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	1.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6983039; hg19: chr8-116330855;