rs702139

Variant names:

• chr9-1564704-A-C
• rs702139

Your query was ambiguous. Multiple possible variants found:

• chr9-1564704-A-C
• chr9-1564704-A-G
• chr9-1564704-A-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 0.667 in 151,942 control chromosomes in the GnomAD database, including 34,266 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 0.67 (34266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.946
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 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: 0.667 AC: 101285 AN: 151824 Hom.: 34230 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.667 AC: 101365 AN: 151942 Hom.: 34266 Cov.: 32 AF XY: 0.671 AC XY: 49827 AN XY: 74274

African (AFR) AF: 0.722 AC: 29902 AN: 41432

American (AMR) AF: 0.687 AC: 10476 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1839 AN: 3466

East Asian (EAS) AF: 0.802 AC: 4147 AN: 5174

South Asian (SAS) AF: 0.492 AC: 2369 AN: 4816

European-Finnish (FIN) AF: 0.743 AC: 7847 AN: 10558

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42624 AN: 67936

Other (OTH) AF: 0.641 AC: 1352 AN: 2110

Alfa AF: 0.633 Hom.: 12349

Bravo AF: 0.670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.7
DANN	Benign	0.70
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs702139; hg19: chr9-1564704; COSMIC: COSV69440883;