rs6980733

Variant names:

• chr8-83826372-T-G
• rs6980733

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 0.37 in 152,072 control chromosomes in the GnomAD database, including 12,308 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 0.37 (12308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 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: 0.370 AC: 56202 AN: 151954 Hom.: 12299 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.370 AC: 56215 AN: 152072 Hom.: 12308 Cov.: 32 AF XY: 0.368 AC XY: 27386 AN XY: 74358

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.384

Alfa AF: 0.418 Hom.: 4925

Bravo AF: 0.353

Asia WGS AF: 0.278 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
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: rs6980733; hg19: chr8-84738607;