rs9892622

Positions:

• chr17-78350041-G-A
• chr17-78350041-G-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 0.505 in 152,000 control chromosomes in the GnomAD database, including 20,397 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 0.50 (20397 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 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: 0.505 AC: 76712 AN: 151882 Hom.: 20395 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.505 AC: 76735 AN: 152000 Hom.: 20397 Cov.: 31 AF XY: 0.508 AC XY: 37721 AN XY: 74294

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.509

Alfa AF: 0.553 Hom.: 23289

Bravo AF: 0.494

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9892622; hg19: chr17-76346122;