rs13037755

Positions:

• chr20-54794480-C-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 0.17 in 152,018 control chromosomes in the GnomAD database, including 2,948 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 0.17 (2948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25882 AN: 151900 Hom.: 2945 Cov.: 33

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.00620

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.170 AC: 25885 AN: 152018 Hom.: 2948 Cov.: 33 AF XY: 0.168 AC XY: 12497 AN XY: 74310

Gnomad4 AFR AF: 0.0455

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.00641

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.136

Alfa AF: 0.195 Hom.: 664

Bravo AF: 0.154

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13037755; hg19: chr20-53411019;