13-104363050-T-C

Variant names:

• chr13-104363050-T-C
• rs1590918

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 0.528 in 151,868 control chromosomes in the GnomAD database, including 23,103 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 0.53 (23103 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 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: 0.528 AC: 80065 AN: 151748 Hom.: 23064 Cov.: 31

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.528 AC: 80164 AN: 151868 Hom.: 23103 Cov.: 31 AF XY: 0.535 AC XY: 39720 AN XY: 74182

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.498

Alfa AF: 0.459 Hom.: 6957

Bravo AF: 0.529

Asia WGS AF: 0.744 AC: 2587 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	1.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1590918; hg19: chr13-105015400;