rs1325803

Variant names:

• chr13-42631133-C-T
• rs1325803

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 0.249 in 152,014 control chromosomes in the GnomAD database, including 5,211 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 0.25 (5211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 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: 0.249 AC: 37808 AN: 151896 Hom.: 5215 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.249 AC: 37801 AN: 152014 Hom.: 5211 Cov.: 32 AF XY: 0.250 AC XY: 18601 AN XY: 74318

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.295

Alfa AF: 0.307 Hom.: 10172

Bravo AF: 0.236

Asia WGS AF: 0.294 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1325803; hg19: chr13-43205269;