13-29735759-T-C

Variant names:

• chr13-29735759-T-C
• rs11147396

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 0.345 in 152,098 control chromosomes in the GnomAD database, including 9,425 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 0.34 (9425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52360 AN: 151980 Hom.: 9411 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.345 AC: 52405 AN: 152098 Hom.: 9425 Cov.: 32 AF XY: 0.344 AC XY: 25539 AN XY: 74336

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.358

Alfa AF: 0.347 Hom.: 4406

Bravo AF: 0.343

Asia WGS AF: 0.506 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11147396; hg19: chr13-30309896;