13-105394164-C-T

Position:

• chr13-105394164-C-T

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 0.323 in 151,810 control chromosomes in the GnomAD database, including 8,285 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 0.32 (8285 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.323 AC: 48963 AN: 151692 Hom.: 8273 Cov.: 30

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.323 AC: 49012 AN: 151810 Hom.: 8285 Cov.: 30 AF XY: 0.325 AC XY: 24080 AN XY: 74180

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.303

Alfa AF: 0.278 Hom.: 6440

Bravo AF: 0.325

Asia WGS AF: 0.264 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7324448; hg19: chr13-106046514;