13-74708758-C-T

Variant names:

• chr13-74708758-C-T
• rs869878

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 0.754 in 152,208 control chromosomes in the GnomAD database, including 43,701 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 0.75 (43701 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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: 0.754 AC: 114693 AN: 152090 Hom.: 43676 Cov.: 34

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.754 AC: 114770 AN: 152208 Hom.: 43701 Cov.: 34 AF XY: 0.760 AC XY: 56553 AN XY: 74410

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.798

Alfa AF: 0.759 Hom.: 59875

Bravo AF: 0.760

Asia WGS AF: 0.857 AC: 2978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs869878; hg19: chr13-75282895;