7-47671190-A-G

Variant names:

• chr7-47671190-A-G
• rs10046555

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 0.846 in 152,122 control chromosomes in the GnomAD database, including 54,586 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 0.85 (54586 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.862 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: 0.846 AC: 128630 AN: 152004 Hom.: 54546 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.846 AC: 128727 AN: 152122 Hom.: 54586 Cov.: 31 AF XY: 0.846 AC XY: 62881 AN XY: 74360

African (AFR) AF: 0.869 AC: 36060 AN: 41490

American (AMR) AF: 0.861 AC: 13139 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2896 AN: 3470

East Asian (EAS) AF: 0.725 AC: 3735 AN: 5152

South Asian (SAS) AF: 0.881 AC: 4241 AN: 4814

European-Finnish (FIN) AF: 0.824 AC: 8735 AN: 10596

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57074 AN: 68018

Other (OTH) AF: 0.857 AC: 1811 AN: 2114

Alfa AF: 0.841 Hom.: 15570

Bravo AF: 0.848

Asia WGS AF: 0.794 AC: 2758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10046555; hg19: chr7-47710788;