13-29735759-T-C

Variant names:

• chr13-29735759-T-C
• rs11147396

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.299 AC: 12415 AN: 41482

American (AMR) AF: 0.310 AC: 4745 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3361 AN: 5166

South Asian (SAS) AF: 0.333 AC: 1603 AN: 4812

European-Finnish (FIN) AF: 0.330 AC: 3491 AN: 10582

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24240 AN: 67974

Other (OTH) AF: 0.358 AC: 757 AN: 2114

Alfa AF: 0.347 Hom.: 4911

Bravo AF: 0.343

Asia WGS AF: 0.506 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs11147396; hg19: chr13-30309896;