rs9915090

Variant names:

• chr17-78145052-T-C
• rs9915090

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;