rs4810542

Variant names:

• chr20-46700103-A-G
• rs4810542

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 0.163 in 152,192 control chromosomes in the GnomAD database, including 2,518 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 0.16 (2518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24689 AN: 152074 Hom.: 2492 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0819

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0912

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.163 AC: 24766 AN: 152192 Hom.: 2518 Cov.: 32 AF XY: 0.166 AC XY: 12345 AN XY: 74404

African (AFR) AF: 0.265 AC: 11001 AN: 41516

American (AMR) AF: 0.195 AC: 2989 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0819 AC: 284 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1486 AN: 5172

South Asian (SAS) AF: 0.182 AC: 878 AN: 4820

European-Finnish (FIN) AF: 0.139 AC: 1474 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0912 AC: 6204 AN: 68018

Other (OTH) AF: 0.141 AC: 299 AN: 2114

Alfa AF: 0.123 Hom.: 165

Bravo AF: 0.170

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.36
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4810542; hg19: chr20-45328742;