rs6581191

chr12-58481915-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 0.436 in 152,038 control chromosomes in the GnomAD database, including 14,856 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 0.44 (14856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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: 0.436 AC: 66169 AN: 151920 Hom.: 14850 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.436 AC: 66215 AN: 152038 Hom.: 14856 Cov.: 32 AF XY: 0.435 AC XY: 32354 AN XY: 74340

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.404

Alfa AF: 0.450 Hom.: 21283

Bravo AF: 0.422

Asia WGS AF: 0.539 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.1
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6581191; hg19: chr12-58875698;