13-68203453-T-C

Position:

• chr13-68203453-T-C

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 0.418 in 152,022 control chromosomes in the GnomAD database, including 14,541 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 0.42 (14541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

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 (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63380 AN: 151904 Hom.: 14500 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.418 AC: 63472 AN: 152022 Hom.: 14541 Cov.: 32 AF XY: 0.417 AC XY: 30995 AN XY: 74306

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.398

Alfa AF: 0.352 Hom.: 19731

Bravo AF: 0.424

Asia WGS AF: 0.490 AC: 1703 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6562520; hg19: chr13-68777585;