12-92978962-A-G

Variant names:

• chr12-92978962-A-G
• rs7302601

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 0.792 in 150,552 control chromosomes in the GnomAD database, including 47,952 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 0.79 (47952 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

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 (AFR) allele frequency at 95% confidence interval = 0.938 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: 0.792 AC: 119103 AN: 150434 Hom.: 47882 Cov.: 24

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.792 AC: 119228 AN: 150552 Hom.: 47952 Cov.: 24 AF XY: 0.792 AC XY: 58172 AN XY: 73426

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.753

Alfa AF: 0.740 Hom.: 22277

Bravo AF: 0.798

Asia WGS AF: 0.792 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7302601; hg19: chr12-93372738;