rs4810544

Variant names:

• chr20-46706399-T-C
• rs4810544

Your query was ambiguous. Multiple possible variants found:

• chr20-46706399-T-C
• chr20-46706399-T-G

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 0.162 in 152,134 control chromosomes in the GnomAD database, including 2,486 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 (2486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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: 0.161 AC: 24522 AN: 152016 Hom.: 2460 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.162 AC: 24599 AN: 152134 Hom.: 2486 Cov.: 32 AF XY: 0.165 AC XY: 12281 AN XY: 74370

African (AFR) AF: 0.261 AC: 10830 AN: 41476

American (AMR) AF: 0.195 AC: 2975 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0818 AC: 284 AN: 3470

East Asian (EAS) AF: 0.293 AC: 1511 AN: 5158

South Asian (SAS) AF: 0.182 AC: 878 AN: 4818

European-Finnish (FIN) AF: 0.139 AC: 1473 AN: 10592

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

European-Non Finnish (NFE) AF: 0.0911 AC: 6197 AN: 68018

Other (OTH) AF: 0.142 AC: 300 AN: 2114

Alfa AF: 0.112 Hom.: 225

Bravo AF: 0.169

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4810544; hg19: chr20-45335038;