rs959066

chr9-102278981-G-Achr9-102278981-G-T

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 0.346 in 151,906 control chromosomes in the GnomAD database, including 9,810 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 0.35 (9810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.345 AC: 52410 AN: 151786 Hom.: 9777 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.346 AC: 52487 AN: 151906 Hom.: 9810 Cov.: 32 AF XY: 0.349 AC XY: 25944 AN XY: 74264

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.315

Alfa AF: 0.277 Hom.: 8446

Bravo AF: 0.346

Asia WGS AF: 0.469 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.59
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs959066; hg19: chr9-105041263;