rs1593812

Positions:

• chr12-103581871-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 0.174 in 152,160 control chromosomes in the GnomAD database, including 2,721 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 (2721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 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: 0.174 AC: 26407 AN: 152042 Hom.: 2717 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.174 AC: 26442 AN: 152160 Hom.: 2721 Cov.: 32 AF XY: 0.176 AC XY: 13087 AN XY: 74392

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.195

Alfa AF: 0.139 Hom.: 3281

Bravo AF: 0.175

Asia WGS AF: 0.337 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1593812; hg19: chr12-103975649;