rs1542176

Variant names:

• chr2-113092260-C-T
• rs1542176

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 0.557 in 151,678 control chromosomes in the GnomAD database, including 24,920 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 0.56 (24920 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 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: 0.557 AC: 84463 AN: 151562 Hom.: 24898 Cov.: 30

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.557 AC: 84541 AN: 151678 Hom.: 24920 Cov.: 30 AF XY: 0.551 AC XY: 40801 AN XY: 74078

African (AFR) AF: 0.767 AC: 31705 AN: 41362

American (AMR) AF: 0.513 AC: 7814 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1599 AN: 3468

East Asian (EAS) AF: 0.347 AC: 1778 AN: 5128

South Asian (SAS) AF: 0.462 AC: 2226 AN: 4814

European-Finnish (FIN) AF: 0.455 AC: 4759 AN: 10466

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32864 AN: 67892

Other (OTH) AF: 0.537 AC: 1129 AN: 2104

Alfa AF: 0.508 Hom.: 71642

Bravo AF: 0.571

Asia WGS AF: 0.460 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.51
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1542176; hg19: chr2-113849837;