17-47497840-G-A

Variant names:

• chr17-47497840-G-A
• rs9901869

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 0.562 in 151,546 control chromosomes in the GnomAD database, including 24,546 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 0.56 (24546 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 29 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 = 0.671 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: 0.562 AC: 85123 AN: 151428 Hom.: 24514 Cov.: 28

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.562 AC: 85218 AN: 151546 Hom.: 24546 Cov.: 28 AF XY: 0.560 AC XY: 41413 AN XY: 74012

African (AFR) AF: 0.678 AC: 28028 AN: 41346

American (AMR) AF: 0.498 AC: 7578 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1930 AN: 3466

East Asian (EAS) AF: 0.625 AC: 3205 AN: 5124

South Asian (SAS) AF: 0.524 AC: 2507 AN: 4786

European-Finnish (FIN) AF: 0.486 AC: 5073 AN: 10428

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35107 AN: 67886

Other (OTH) AF: 0.549 AC: 1152 AN: 2100

Alfa AF: 0.523 Hom.: 12472

Bravo AF: 0.566

Asia WGS AF: 0.515 AC: 1793 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	0.61
DANN	Benign	0.70
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9901869; hg19: chr17-45575206;