7-9510942-A-C

Variant names:

• chr7-9510942-A-C
• rs12702919

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 0.545 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
• Publications: 2 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 = 0.822 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.462 AC: 19125 AN: 41358

American (AMR) AF: 0.514 AC: 7788 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1989 AN: 3458

East Asian (EAS) AF: 0.843 AC: 4324 AN: 5130

South Asian (SAS) AF: 0.510 AC: 2459 AN: 4818

European-Finnish (FIN) AF: 0.680 AC: 7117 AN: 10472

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 37850 AN: 67540

Other (OTH) AF: 0.572 AC: 1202 AN: 2102

Alfa AF: 0.524 Hom.: 4756

Bravo AF: 0.535

Asia WGS AF: 0.685 AC: 2356 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.73
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12702919; hg19: chr7-9550572;