7-150987460-A-G

Variant names:

• chr7-150987460-A-G
• rs6946415

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 0.726 in 151,728 control chromosomes in the GnomAD database, including 41,152 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 0.73 (41152 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 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: 0.726 AC: 110000 AN: 151608 Hom.: 41088 Cov.: 29

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.726 AC: 110122 AN: 151728 Hom.: 41152 Cov.: 29 AF XY: 0.728 AC XY: 53984 AN XY: 74142

African (AFR) AF: 0.893 AC: 37012 AN: 41428

American (AMR) AF: 0.716 AC: 10946 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3468

East Asian (EAS) AF: 0.889 AC: 4543 AN: 5112

South Asian (SAS) AF: 0.775 AC: 3720 AN: 4800

European-Finnish (FIN) AF: 0.656 AC: 6891 AN: 10512

Middle Eastern (MID) AF: 0.663 AC: 191 AN: 288

European-Non Finnish (NFE) AF: 0.625 AC: 42396 AN: 67826

Other (OTH) AF: 0.692 AC: 1456 AN: 2104

Alfa AF: 0.676 Hom.: 7423

Bravo AF: 0.740

Asia WGS AF: 0.835 AC: 2905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.61
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs6946415; hg19: chr7-150684548;