rs7295242

Variant names:

• chr12-85305039-G-A
• rs7295242

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 0.169 in 152,026 control chromosomes in the GnomAD database, including 3,771 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 0.17 (3771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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: 0.169 AC: 25703 AN: 151906 Hom.: 3757 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0523

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.169 AC: 25756 AN: 152026 Hom.: 3771 Cov.: 32 AF XY: 0.174 AC XY: 12928 AN XY: 74302

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0523

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.0772

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.0524

Gnomad4 OTH AF: 0.139

Alfa AF: 0.0712 Hom.: 826

Bravo AF: 0.180

Asia WGS AF: 0.244 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7295242; hg19: chr12-85698817;