7-150633857-G-A

Variant names:

• chr7-150633857-G-A
• rs6946579

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 0.704 in 152,102 control chromosomes in the GnomAD database, including 37,874 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 0.70 (37874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106975 AN: 151984 Hom.: 37826 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.704 AC: 107084 AN: 152102 Hom.: 37874 Cov.: 32 AF XY: 0.711 AC XY: 52852 AN XY: 74372

African (AFR) AF: 0.760 AC: 31523 AN: 41480

American (AMR) AF: 0.688 AC: 10519 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2159 AN: 3470

East Asian (EAS) AF: 0.718 AC: 3707 AN: 5166

South Asian (SAS) AF: 0.768 AC: 3701 AN: 4820

European-Finnish (FIN) AF: 0.794 AC: 8405 AN: 10592

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44874 AN: 67974

Other (OTH) AF: 0.661 AC: 1394 AN: 2110

Alfa AF: 0.679 Hom.: 5982

Bravo AF: 0.696

Asia WGS AF: 0.772 AC: 2685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.20
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6946579; hg19: chr7-150330945;