13-68783652-T-C

Position:

• chr13-68783652-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 0.24 in 151,972 control chromosomes in the GnomAD database, including 4,535 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 0.24 (4535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.261 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: 0.240 AC: 36416 AN: 151854 Hom.: 4531 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0273

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.240 AC: 36438 AN: 151972 Hom.: 4535 Cov.: 32 AF XY: 0.235 AC XY: 17490 AN XY: 74270

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.0274

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.252

Alfa AF: 0.234 Hom.: 548

Bravo AF: 0.244

Asia WGS AF: 0.104 AC: 359 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1507203; hg19: chr13-69357784;