rs545125

Variant names:

• chr8-52938902-T-C
• rs545125

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 0.567 in 152,024 control chromosomes in the GnomAD database, including 24,774 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 0.57 (24774 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.665 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: 0.567 AC: 86060 AN: 151902 Hom.: 24733 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.565

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.567 AC: 86152 AN: 152020 Hom.: 24774 Cov.: 33 AF XY: 0.571 AC XY: 42396 AN XY: 74302

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.570

Alfa AF: 0.541 Hom.: 35268

Bravo AF: 0.565

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs545125; hg19: chr8-53851462;