rs7770969

Variant names:

• chr6-80960392-G-T
• rs7770969

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.372 AC: 15353 AN: 41322

American (AMR) AF: 0.304 AC: 4602 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3460

East Asian (EAS) AF: 0.558 AC: 2841 AN: 5094

South Asian (SAS) AF: 0.429 AC: 2060 AN: 4806

European-Finnish (FIN) AF: 0.406 AC: 4261 AN: 10496

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23815 AN: 67672

Other (OTH) AF: 0.359 AC: 757 AN: 2106

Alfa AF: 0.357 Hom.: 1252

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
PhyloP100		-0.045

Splicing

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

Other links and lift over

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