13-20209879-C-T

Variant names:

• chr13-20209879-C-T
• rs9315384

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 0.664 in 152,126 control chromosomes in the GnomAD database, including 36,732 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 0.66 (36732 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100935 AN: 152006 Hom.: 36736 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.664 AC: 100954 AN: 152126 Hom.: 36732 Cov.: 33 AF XY: 0.667 AC XY: 49633 AN XY: 74362

African (AFR) AF: 0.350 AC: 14507 AN: 41462

American (AMR) AF: 0.641 AC: 9797 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2554 AN: 3470

East Asian (EAS) AF: 0.579 AC: 2992 AN: 5170

South Asian (SAS) AF: 0.852 AC: 4104 AN: 4818

European-Finnish (FIN) AF: 0.883 AC: 9352 AN: 10596

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55407 AN: 68010

Other (OTH) AF: 0.672 AC: 1419 AN: 2112

Alfa AF: 0.698 Hom.: 13162

Bravo AF: 0.626

Asia WGS AF: 0.712 AC: 2476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.39
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs9315384; hg19: chr13-20784018;