chr13-59415033-T-C

Position:

• chr13-59415033-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 0.177 in 152,186 control chromosomes in the GnomAD database, including 2,494 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 0.18 (2494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26961 AN: 152068 Hom.: 2492 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.177 AC: 26984 AN: 152186 Hom.: 2494 Cov.: 32 AF XY: 0.176 AC XY: 13084 AN XY: 74412

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0411

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.179

Alfa AF: 0.193 Hom.: 3975

Bravo AF: 0.177

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7996198; hg19: chr13-59989167;