rs845542

Variant names:

• chr3-55458022-C-T
• rs845542

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 0.8 in 152,200 control chromosomes in the GnomAD database, including 48,882 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 0.80 (48882 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 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: 0.800 AC: 121635 AN: 152082 Hom.: 48847 Cov.: 33

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.800 AC: 121718 AN: 152200 Hom.: 48882 Cov.: 33 AF XY: 0.799 AC XY: 59494 AN XY: 74418

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.797

Alfa AF: 0.775 Hom.: 6679

Bravo AF: 0.810

Asia WGS AF: 0.809 AC: 2812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845542; hg19: chr3-55492050;