13-20375953-G-A

Position:

• chr13-20375953-G-A

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 0.0909 in 152,168 control chromosomes in the GnomAD database, including 920 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 0.091 (920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 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: 0.0909 AC: 13827 AN: 152050 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0909 AC: 13829 AN: 152168 Hom.: 920 Cov.: 32 AF XY: 0.0932 AC XY: 6936 AN XY: 74398

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0895

Gnomad4 NFE AF: 0.0975

Gnomad4 OTH AF: 0.105

Alfa AF: 0.100 Hom.: 562

Bravo AF: 0.0921

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9550642; hg19: chr13-20950092;