chr13-38465795-T-C

Variant names:

• chr13-38465795-T-C
• rs980285

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 0.546 in 151,808 control chromosomes in the GnomAD database, including 23,967 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 0.55 (23967 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 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: 0.547 AC: 82898 AN: 151688 Hom.: 23962 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.546 AC: 82916 AN: 151808 Hom.: 23967 Cov.: 31 AF XY: 0.545 AC XY: 40440 AN XY: 74184

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.529

Alfa AF: 0.613 Hom.: 3646

Bravo AF: 0.524

Asia WGS AF: 0.357 AC: 1232 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs980285; hg19: chr13-39039932; COSMIC: COSV69347495;