rs9909172

Variant names:

• chr17-43710153-T-C
• rs9909172

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 0.519 in 152,120 control chromosomes in the GnomAD database, including 22,654 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 0.52 (22654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.775 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: 0.519 AC: 78827 AN: 152002 Hom.: 22609 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.519 AC: 78916 AN: 152120 Hom.: 22654 Cov.: 32 AF XY: 0.520 AC XY: 38678 AN XY: 74352

African (AFR) AF: 0.782 AC: 32444 AN: 41490

American (AMR) AF: 0.484 AC: 7403 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1500 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1723 AN: 5172

South Asian (SAS) AF: 0.423 AC: 2040 AN: 4826

European-Finnish (FIN) AF: 0.507 AC: 5366 AN: 10574

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26998 AN: 67984

Other (OTH) AF: 0.474 AC: 1000 AN: 2110

Alfa AF: 0.500 Hom.: 2674

Bravo AF: 0.530

Asia WGS AF: 0.358 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.82
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs9909172; hg19: chr17-41787521;