rs2158390

Variant names:

• chr12-112905570-C-G
• rs2158390

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 0.846 in 152,176 control chromosomes in the GnomAD database, including 55,080 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 0.85 (55080 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.846 AC: 128648 AN: 152058 Hom.: 55031 Cov.: 31

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.846 AC: 128763 AN: 152176 Hom.: 55080 Cov.: 31 AF XY: 0.845 AC XY: 62833 AN XY: 74368

African (AFR) AF: 0.964 AC: 40061 AN: 41546

American (AMR) AF: 0.853 AC: 13044 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2339 AN: 3468

East Asian (EAS) AF: 0.993 AC: 5138 AN: 5174

South Asian (SAS) AF: 0.752 AC: 3624 AN: 4822

European-Finnish (FIN) AF: 0.797 AC: 8407 AN: 10554

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53466 AN: 68000

Other (OTH) AF: 0.840 AC: 1774 AN: 2112

Alfa AF: 0.822 Hom.: 6404

Bravo AF: 0.859

Asia WGS AF: 0.872 AC: 3031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.50
PhyloP100		-0.83
PromoterAI		0.016	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2158390; hg19: chr12-113343375;