rs12702919

Variant names:

• chr7-9510942-A-C
• rs12702919

Your query was ambiguous. Multiple possible variants found:

• chr7-9510942-A-C
• chr7-9510942-A-G
• chr7-9510942-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 0.545 in 151,222 control chromosomes in the GnomAD database, including 23,002 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 0.55 (23002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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 = 0.822 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: 0.545 AC: 82370 AN: 151100 Hom.: 22985 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.545 AC: 82430 AN: 151222 Hom.: 23002 Cov.: 32 AF XY: 0.551 AC XY: 40711 AN XY: 73874

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.572

Alfa AF: 0.555 Hom.: 3016

Bravo AF: 0.535

Asia WGS AF: 0.685 AC: 2356 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12702919; hg19: chr7-9550572;