rs1780615

chr20-38342716-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.592

Alfa AF: 0.638 Hom.: 3864

Bravo AF: 0.610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1780615; hg19: chr20-36971119;