chr13-105815706-C-T

Variant names:

• chr13-105815706-C-T
• rs1328089

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 0.669 in 152,024 control chromosomes in the GnomAD database, including 35,166 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 0.67 (35166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 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: 0.670 AC: 101727 AN: 151906 Hom.: 35175 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.669 AC: 101743 AN: 152024 Hom.: 35166 Cov.: 32 AF XY: 0.670 AC XY: 49772 AN XY: 74288

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.665

Alfa AF: 0.729 Hom.: 74819

Bravo AF: 0.650

Asia WGS AF: 0.649 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328089; hg19: chr13-106468055;