7-46764858-A-G

Variant names:

• chr7-46764858-A-G
• rs6944447

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 0.811 in 151,982 control chromosomes in the GnomAD database, including 50,471 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 0.81 (50471 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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: 0.811 AC: 123184 AN: 151864 Hom.: 50420 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.811 AC: 123290 AN: 151982 Hom.: 50471 Cov.: 31 AF XY: 0.813 AC XY: 60387 AN XY: 74274

African (AFR) AF: 0.930 AC: 38567 AN: 41482

American (AMR) AF: 0.843 AC: 12865 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2687 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4394 AN: 5146

South Asian (SAS) AF: 0.778 AC: 3735 AN: 4798

European-Finnish (FIN) AF: 0.749 AC: 7903 AN: 10556

Middle Eastern (MID) AF: 0.703 AC: 204 AN: 290

European-Non Finnish (NFE) AF: 0.746 AC: 50675 AN: 67958

Other (OTH) AF: 0.796 AC: 1677 AN: 2106

Alfa AF: 0.782 Hom.: 75732

Bravo AF: 0.823

Asia WGS AF: 0.825 AC: 2870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.73
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs6944447; hg19: chr7-46804456;