chr3-55458022-C-T

Variant names:

• chr3-55458022-C-T
• rs845542

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 0.8 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.880 AC: 36573 AN: 41540

American (AMR) AF: 0.845 AC: 12920 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2755 AN: 3472

East Asian (EAS) AF: 0.776 AC: 4003 AN: 5160

South Asian (SAS) AF: 0.824 AC: 3978 AN: 4826

European-Finnish (FIN) AF: 0.748 AC: 7928 AN: 10600

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50874 AN: 67988

Other (OTH) AF: 0.797 AC: 1683 AN: 2112

Alfa AF: 0.778 Hom.: 6986

Bravo AF: 0.810

Asia WGS AF: 0.809 AC: 2812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.72
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs845542; hg19: chr3-55492050;