rs7295750

Variant names:

• chr12-107143893-A-G
• rs7295750

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 0.662 in 152,148 control chromosomes in the GnomAD database, including 33,598 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 0.66 (33598 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.662 AC: 100665 AN: 152030 Hom.: 33553 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.662 AC: 100767 AN: 152148 Hom.: 33598 Cov.: 33 AF XY: 0.666 AC XY: 49584 AN XY: 74396

African (AFR) AF: 0.641 AC: 26583 AN: 41498

American (AMR) AF: 0.665 AC: 10167 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2014 AN: 3472

East Asian (EAS) AF: 0.942 AC: 4881 AN: 5184

South Asian (SAS) AF: 0.644 AC: 3103 AN: 4822

European-Finnish (FIN) AF: 0.674 AC: 7123 AN: 10574

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44835 AN: 67998

Other (OTH) AF: 0.655 AC: 1384 AN: 2112

Alfa AF: 0.652 Hom.: 16437

Bravo AF: 0.662

Asia WGS AF: 0.765 AC: 2661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.70
DANN	Benign	0.81
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7295750; hg19: chr12-107537671;