rs959066

Variant names:

• chr9-102278981-G-A
• rs959066

Your query was ambiguous. Multiple possible variants found:

• chr9-102278981-G-A
• chr9-102278981-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.465 AC: 19241 AN: 41408

American (AMR) AF: 0.324 AC: 4953 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 807 AN: 3466

East Asian (EAS) AF: 0.580 AC: 2981 AN: 5136

South Asian (SAS) AF: 0.423 AC: 2039 AN: 4816

European-Finnish (FIN) AF: 0.304 AC: 3210 AN: 10562

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18110 AN: 67932

Other (OTH) AF: 0.315 AC: 666 AN: 2114

Alfa AF: 0.283 Hom.: 11144

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
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs959066; hg19: chr9-105041263;