13-100039113-T-C

Variant names:

• chr13-100039113-T-C
• rs8000973

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 0.486 in 151,762 control chromosomes in the GnomAD database, including 18,423 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 0.49 (18423 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 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: 0.486 AC: 73723 AN: 151644 Hom.: 18400 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.486 AC: 73801 AN: 151762 Hom.: 18423 Cov.: 31 AF XY: 0.477 AC XY: 35398 AN XY: 74160

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.539

Alfa AF: 0.475 Hom.: 6991

Bravo AF: 0.495

Asia WGS AF: 0.274 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8000973; hg19: chr13-100691367;