rs11925054

Variant names:

• chr3-55356858-G-T
• rs11925054

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 0.0971 in 152,226 control chromosomes in the GnomAD database, including 856 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 0.097 (856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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: 0.0971 AC: 14777 AN: 152108 Hom.: 857 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0971 AC: 14774 AN: 152226 Hom.: 856 Cov.: 32 AF XY: 0.0932 AC XY: 6935 AN XY: 74424

Gnomad4 AFR AF: 0.0488

Gnomad4 AMR AF: 0.0917

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.0578

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.111

Alfa AF: 0.128 Hom.: 1260

Bravo AF: 0.0960

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.44
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11925054; hg19: chr3-55390886;