rs9909172

Positions:

• chr17-43710153-T-C

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 0.519 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.474

Alfa AF: 0.488 Hom.: 2427

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9909172; hg19: chr17-41787521;