rs2025543

Variant names:

• chr9-112938844-G-A
• rs2025543

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 0.972 in 152,328 control chromosomes in the GnomAD database, including 72,029 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 0.97 (72029 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 0 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 (AMR) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.972 AC: 147998 AN: 152210 Hom.: 71975 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.972 AC: 148110 AN: 152328 Hom.: 72029 Cov.: 32 AF XY: 0.974 AC XY: 72524 AN XY: 74482

African (AFR) AF: 0.962 AC: 39981 AN: 41576

American (AMR) AF: 0.987 AC: 15111 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.971 AC: 3371 AN: 3470

East Asian (EAS) AF: 0.934 AC: 4836 AN: 5176

South Asian (SAS) AF: 0.967 AC: 4669 AN: 4826

European-Finnish (FIN) AF: 0.987 AC: 10482 AN: 10616

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.976 AC: 66425 AN: 68038

Other (OTH) AF: 0.967 AC: 2044 AN: 2114

Alfa AF: 0.973 Hom.: 93688

Bravo AF: 0.972

Asia WGS AF: 0.939 AC: 3263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.54
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2025543; hg19: chr9-115701124;