rs7967594

Positions:

• chr12-84572395-A-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;