rs545125

Positions:

• chr8-52938902-T-C

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/exons	MANE	UniProt

Ensembl

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