7-46775939-G-A

Variant names:

• chr7-46775939-G-A
• rs1404719

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 0.458 in 151,862 control chromosomes in the GnomAD database, including 16,159 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 0.46 (16159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• 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 = 0.511 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: 0.458 AC: 69432 AN: 151744 Hom.: 16145 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.458 AC: 69485 AN: 151862 Hom.: 16159 Cov.: 32 AF XY: 0.460 AC XY: 34125 AN XY: 74200

African (AFR) AF: 0.517 AC: 21426 AN: 41438

American (AMR) AF: 0.478 AC: 7286 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3466

East Asian (EAS) AF: 0.452 AC: 2333 AN: 5156

South Asian (SAS) AF: 0.502 AC: 2412 AN: 4808

European-Finnish (FIN) AF: 0.455 AC: 4789 AN: 10524

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.418 AC: 28407 AN: 67902

Other (OTH) AF: 0.460 AC: 971 AN: 2110

Alfa AF: 0.433 Hom.: 39469

Bravo AF: 0.464

Asia WGS AF: 0.496 AC: 1725 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	3.9
DANN	Benign	0.51
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1404719; hg19: chr7-46815537;