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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.641

Alfa AF: 0.620 Hom.: 7032

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

Splicing

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

Publications

LitVar

Other links and lift over

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