rs13044826

Variant names:

• chr20-45173224-G-A
• rs13044826

Your query was ambiguous. Multiple possible variants found:

• chr20-45173224-G-A
• chr20-45173224-G-T

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 0.153 in 152,186 control chromosomes in the GnomAD database, including 1,904 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 0.15 (1904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 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: 0.153 AC: 23201 AN: 152068 Hom.: 1899 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.153 AC: 23240 AN: 152186 Hom.: 1904 Cov.: 32 AF XY: 0.154 AC XY: 11447 AN XY: 74396

African (AFR) AF: 0.122 AC: 5085 AN: 41536

American (AMR) AF: 0.130 AC: 1987 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3470

East Asian (EAS) AF: 0.0340 AC: 176 AN: 5178

South Asian (SAS) AF: 0.146 AC: 705 AN: 4816

European-Finnish (FIN) AF: 0.190 AC: 2016 AN: 10588

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11838 AN: 67978

Other (OTH) AF: 0.168 AC: 355 AN: 2116

Alfa AF: 0.138 Hom.: 746

Bravo AF: 0.146

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13044826; hg19: chr20-43801865;