rs9901643

Variant names:

• chr17-7516507-G-A
• rs9901643

Your query was ambiguous. Multiple possible variants found:

• chr17-7516507-G-A
• chr17-7516507-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.172 in 151,316 control chromosomes in the GnomAD database, including 2,686 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 0.17 (2686 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26028 AN: 151210 Hom.: 2670 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.172 AC: 26064 AN: 151316 Hom.: 2686 Cov.: 31 AF XY: 0.182 AC XY: 13463 AN XY: 73834

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.161

Alfa AF: 0.145 Hom.: 2374

Bravo AF: 0.164

Asia WGS AF: 0.339 AC: 1176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9901643; hg19: chr17-7419824;