13-105944370-C-T

Variant names:

• chr13-105944370-C-T
• rs488248

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 0.698 in 152,004 control chromosomes in the GnomAD database, including 37,482 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 0.70 (37482 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

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 (EAS) allele frequency at 95% confidence interval = 0.827 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: 0.698 AC: 105990 AN: 151886 Hom.: 37454 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.698 AC: 106065 AN: 152004 Hom.: 37482 Cov.: 31 AF XY: 0.700 AC XY: 51982 AN XY: 74292

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.744

Alfa AF: 0.715 Hom.: 29913

Bravo AF: 0.707

Asia WGS AF: 0.804 AC: 2796 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	1.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs488248; hg19: chr13-106596719;