chr13-109751112-T-C

Position:

• chr13-109751112-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 0.399 in 151,810 control chromosomes in the GnomAD database, including 13,039 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 0.40 (13039 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 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: 0.399 AC: 60585 AN: 151694 Hom.: 13044 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.399 AC: 60584 AN: 151810 Hom.: 13039 Cov.: 31 AF XY: 0.402 AC XY: 29840 AN XY: 74160

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.441

Alfa AF: 0.400 Hom.: 1777

Bravo AF: 0.379

Asia WGS AF: 0.383 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4773082; hg19: chr13-110403459;