rs6467970

Variant names:

• chr7-83872939-A-G
• rs6467970

Your query was ambiguous. Multiple possible variants found:

• chr7-83872939-A-G
• chr7-83872939-A-T

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 0.266 in 151,956 control chromosomes in the GnomAD database, including 7,478 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 0.27 (7478 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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: 0.265 AC: 40297 AN: 151838 Hom.: 7452 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.266 AC: 40374 AN: 151956 Hom.: 7478 Cov.: 32 AF XY: 0.265 AC XY: 19708 AN XY: 74266

African (AFR) AF: 0.474 AC: 19609 AN: 41402

American (AMR) AF: 0.278 AC: 4243 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.687 AC: 3528 AN: 5136

South Asian (SAS) AF: 0.194 AC: 936 AN: 4818

European-Finnish (FIN) AF: 0.112 AC: 1182 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9546 AN: 67982

Other (OTH) AF: 0.291 AC: 615 AN: 2112

Alfa AF: 0.181 Hom.: 5274

Bravo AF: 0.292

Asia WGS AF: 0.462 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.56
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs6467970; hg19: chr7-83502255;