rs9915090

chr17-78145052-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 0.657 in 152,156 control chromosomes in the GnomAD database, including 33,312 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 0.66 (33312 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 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: 0.657 AC: 99817 AN: 152038 Hom.: 33255 Cov.: 34

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.657 AC: 99937 AN: 152156 Hom.: 33312 Cov.: 34 AF XY: 0.659 AC XY: 48994 AN XY: 74374

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.679

Alfa AF: 0.625 Hom.: 36557

Bravo AF: 0.666

Asia WGS AF: 0.568 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9915090; hg19: chr17-76141133;