rs1325803

Variant names:

• chr13-42631133-C-T
• rs1325803

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.129 AC: 5365 AN: 41450

American (AMR) AF: 0.230 AC: 3518 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3472

East Asian (EAS) AF: 0.144 AC: 743 AN: 5168

South Asian (SAS) AF: 0.430 AC: 2073 AN: 4820

European-Finnish (FIN) AF: 0.278 AC: 2933 AN: 10550

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20908 AN: 67968

Other (OTH) AF: 0.295 AC: 622 AN: 2108

Alfa AF: 0.299 Hom.: 12214

Bravo AF: 0.236

Asia WGS AF: 0.294 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.1
DANN	Benign	0.65
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1325803; hg19: chr13-43205269;