chr20-38342716-A-T

Variant names:

• chr20-38342716-A-T
• rs1780615

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 0.622 in 152,136 control chromosomes in the GnomAD database, including 29,625 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 0.62 (29625 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.645 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: 0.623 AC: 94640 AN: 152018 Hom.: 29613 Cov.: 33

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.622 AC: 94690 AN: 152136 Hom.: 29625 Cov.: 33 AF XY: 0.621 AC XY: 46170 AN XY: 74364

African (AFR) AF: 0.603 AC: 25032 AN: 41498

American (AMR) AF: 0.576 AC: 8801 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1972 AN: 3472

East Asian (EAS) AF: 0.544 AC: 2813 AN: 5174

South Asian (SAS) AF: 0.664 AC: 3198 AN: 4816

European-Finnish (FIN) AF: 0.633 AC: 6696 AN: 10574

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44120 AN: 67998

Other (OTH) AF: 0.592 AC: 1251 AN: 2114

Alfa AF: 0.638 Hom.: 3864

Bravo AF: 0.610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1780615; hg19: chr20-36971119;