13-37305031-C-T

Variant names:

• chr13-37305031-C-T
• rs1324038

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 0.58 in 151,754 control chromosomes in the GnomAD database, including 25,669 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 0.58 (25669 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.647 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: 0.580 AC: 87922 AN: 151638 Hom.: 25659 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.580 AC: 87968 AN: 151754 Hom.: 25669 Cov.: 31 AF XY: 0.580 AC XY: 43013 AN XY: 74156

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.602

Alfa AF: 0.602 Hom.: 11264

Bravo AF: 0.565

Asia WGS AF: 0.631 AC: 2196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324038; hg19: chr13-37879168; COSMIC: COSV65945600;