rs6983777

Variant names:

• chr8-103106338-A-G
• rs6983777

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 0.508 in 152,040 control chromosomes in the GnomAD database, including 19,898 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 0.51 (19898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 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: 0.508 AC: 77237 AN: 151922 Hom.: 19883 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.508 AC: 77288 AN: 152040 Hom.: 19898 Cov.: 32 AF XY: 0.507 AC XY: 37660 AN XY: 74318

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.510

Alfa AF: 0.504 Hom.: 11792

Bravo AF: 0.517

Asia WGS AF: 0.418 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6983777; hg19: chr8-104118566;