rs2025543

chr9-112938844-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.987

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.976

Gnomad4 OTH AF: 0.967

Alfa AF: 0.976 Hom.: 9309

Bravo AF: 0.972

Asia WGS AF: 0.939 AC: 3263 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	0.61
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2025543; hg19: chr9-115701124;