chr13-97507450-T-C

Variant names:

• chr13-97507450-T-C
• rs9513249

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 0.693 in 152,052 control chromosomes in the GnomAD database, including 37,325 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 0.69 (37325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 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: 0.693 AC: 105298 AN: 151932 Hom.: 37305 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.693 AC: 105360 AN: 152052 Hom.: 37325 Cov.: 31 AF XY: 0.692 AC XY: 51457 AN XY: 74326

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.736

Alfa AF: 0.760 Hom.: 95883

Bravo AF: 0.684

Asia WGS AF: 0.589 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9513249; hg19: chr13-98159704;