rs9891455

Positions:

• chr17-32132039-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 0.267 in 152,118 control chromosomes in the GnomAD database, including 6,994 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 0.27 (6994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40524 AN: 152000 Hom.: 6962 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.267 AC: 40608 AN: 152118 Hom.: 6994 Cov.: 32 AF XY: 0.264 AC XY: 19614 AN XY: 74384

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.240

Alfa AF: 0.228 Hom.: 818

Bravo AF: 0.281

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9891455; hg19: chr17-30459058;