20-23355795-T-G

Variant names:

• chr20-23355795-T-G
• rs1419005

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 0.286 in 152,136 control chromosomes in the GnomAD database, including 6,485 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 0.29 (6485 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 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: 0.286 AC: 43516 AN: 152018 Hom.: 6484 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.286 AC: 43528 AN: 152136 Hom.: 6485 Cov.: 33 AF XY: 0.289 AC XY: 21476 AN XY: 74376

African (AFR) AF: 0.193 AC: 8025 AN: 41500

American (AMR) AF: 0.339 AC: 5179 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1667 AN: 5176

South Asian (SAS) AF: 0.280 AC: 1351 AN: 4818

European-Finnish (FIN) AF: 0.304 AC: 3226 AN: 10598

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22025 AN: 67980

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.289 Hom.: 3643

Bravo AF: 0.288

Asia WGS AF: 0.290 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.65
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1419005; hg19: chr20-23336432;