rs12702919

chr7-9510942-A-Cchr7-9510942-A-Gchr7-9510942-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;