rs12054895

Variant names:

• chr5-27611324-G-T
• rs12054895

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 0.251 in 151,858 control chromosomes in the GnomAD database, including 6,240 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 0.25 (6240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 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: 0.251 AC: 38070 AN: 151740 Hom.: 6236 Cov.: 32

Gnomad AFR AF: 0.0906

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.251 AC: 38086 AN: 151858 Hom.: 6240 Cov.: 32 AF XY: 0.257 AC XY: 19045 AN XY: 74216

Gnomad4 AFR AF: 0.0903

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.229

Alfa AF: 0.280 Hom.: 2775

Bravo AF: 0.245

Asia WGS AF: 0.492 AC: 1707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.31
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12054895; hg19: chr5-27611431;