rs1593812

Variant names:

• chr12-103581871-A-G
• rs1593812

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.260 AC: 10782 AN: 41480

American (AMR) AF: 0.139 AC: 2121 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1411 AN: 5168

South Asian (SAS) AF: 0.308 AC: 1488 AN: 4826

European-Finnish (FIN) AF: 0.126 AC: 1339 AN: 10600

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.120 AC: 8129 AN: 68006

Other (OTH) AF: 0.195 AC: 413 AN: 2114

Alfa AF: 0.146 Hom.: 5382

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1593812; hg19: chr12-103975649;