rs7967594

Variant names:

• chr12-84572395-A-C
• rs7967594

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 0.533 in 151,858 control chromosomes in the GnomAD database, including 22,686 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 0.53 (22686 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 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: 0.533 AC: 80925 AN: 151740 Hom.: 22684 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.533 AC: 80966 AN: 151858 Hom.: 22686 Cov.: 31 AF XY: 0.537 AC XY: 39881 AN XY: 74232

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.509

Alfa AF: 0.570 Hom.: 50705

Bravo AF: 0.512

Asia WGS AF: 0.579 AC: 2012 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	0.91
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7967594; hg19: chr12-84966174;