rs12115442

Variant names:

• chr9-112943825-G-T
• rs12115442

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 0.028 in 147,862 control chromosomes in the GnomAD database, including 112 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 0.028 (112 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0684 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: 0.0280 AC: 4135 AN: 147756 Hom.: 111 Cov.: 25

Gnomad AFR AF: 0.0706

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0153

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.00273

Gnomad MID AF: 0.0483

Gnomad NFE AF: 0.00783

Gnomad OTH AF: 0.0255

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

GnomAD4 genome AF: 0.0280 AC: 4144 AN: 147862 Hom.: 112 Cov.: 25 AF XY: 0.0277 AC XY: 1983 AN XY: 71596

African (AFR) AF: 0.0706 AC: 2835 AN: 40176

American (AMR) AF: 0.0153 AC: 218 AN: 14230

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3460

East Asian (EAS) AF: 0.0683 AC: 339 AN: 4964

South Asian (SAS) AF: 0.0147 AC: 69 AN: 4698

European-Finnish (FIN) AF: 0.00273 AC: 26 AN: 9528

Middle Eastern (MID) AF: 0.0519 AC: 14 AN: 270

European-Non Finnish (NFE) AF: 0.00781 AC: 528 AN: 67570

Other (OTH) AF: 0.0267 AC: 55 AN: 2058

Alfa AF: 0.0179 Hom.: 12

Bravo AF: 0.0305

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.77
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs12115442; hg19: chr9-115706105;