rs7770969

Variant names:

• chr6-80960392-G-T
• rs7770969

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 0.365 in 151,270 control chromosomes in the GnomAD database, including 10,176 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 0.36 (10176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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: 0.365 AC: 55143 AN: 151152 Hom.: 10148 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.365 AC: 55211 AN: 151270 Hom.: 10176 Cov.: 32 AF XY: 0.370 AC XY: 27320 AN XY: 73896

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.359

Alfa AF: 0.356 Hom.: 1183

Bravo AF: 0.356

Asia WGS AF: 0.455 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7770969; hg19: chr6-81670109; COSMIC: COSV68670063;