rs1558726

Variant names:

• chr12-97282457-G-A
• rs1558726

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 0.078 in 152,168 control chromosomes in the GnomAD database, including 656 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 0.078 (656 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 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: 0.0780 AC: 11853 AN: 152050 Hom.: 653 Cov.: 31

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0858

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

GnomAD4 genome AF: 0.0780 AC: 11864 AN: 152168 Hom.: 656 Cov.: 31 AF XY: 0.0776 AC XY: 5772 AN XY: 74384

African (AFR) AF: 0.0187 AC: 777 AN: 41520

American (AMR) AF: 0.155 AC: 2363 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0878 AC: 305 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0812 AC: 392 AN: 4826

European-Finnish (FIN) AF: 0.0718 AC: 760 AN: 10592

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.103 AC: 6998 AN: 68006

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0924 Hom.: 359

Bravo AF: 0.0807

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs1558726; hg19: chr12-97676235;