rs545125

Variant names:

• chr8-52938902-T-C
• rs545125

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.638 AC: 26436 AN: 41466

American (AMR) AF: 0.554 AC: 8467 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2217 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2484 AN: 5164

South Asian (SAS) AF: 0.685 AC: 3301 AN: 4820

European-Finnish (FIN) AF: 0.540 AC: 5700 AN: 10550

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35581 AN: 67960

Other (OTH) AF: 0.570 AC: 1205 AN: 2114

Alfa AF: 0.539 Hom.: 83350

Bravo AF: 0.565

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.64
PhyloP100		-0.095
PromoterAI		-0.0048	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs545125; hg19: chr8-53851462;