rs7295750

chr12-107143893-A-G

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 0.662 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.655

Alfa AF: 0.651 Hom.: 14605

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7295750; hg19: chr12-107537671;