rs6980733

Positions:

• chr8-83826372-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;