rs9901283

Variant names:

• chr17-74841693-G-A
• rs9901283

Your query was ambiguous. Multiple possible variants found:

• chr17-74841693-G-A
• chr17-74841693-G-C

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 0.566 in 152,166 control chromosomes in the GnomAD database, including 25,160 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 0.57 (25160 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86130 AN: 152048 Hom.: 25154 Cov.: 34

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.566 AC: 86161 AN: 152166 Hom.: 25160 Cov.: 34 AF XY: 0.565 AC XY: 42062 AN XY: 74396

African (AFR) AF: 0.483 AC: 20034 AN: 41514

American (AMR) AF: 0.572 AC: 8749 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1713 AN: 5180

South Asian (SAS) AF: 0.457 AC: 2207 AN: 4832

European-Finnish (FIN) AF: 0.642 AC: 6803 AN: 10598

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43078 AN: 67964

Other (OTH) AF: 0.537 AC: 1134 AN: 2110

Alfa AF: 0.605 Hom.: 39034

Bravo AF: 0.557

Asia WGS AF: 0.411 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	18
DANN	Benign	0.67
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs9901283; hg19: chr17-72837832;