13-32807106-T-C

Variant names:

• chr13-32807106-T-C
• rs4942925

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 0.363 in 152,106 control chromosomes in the GnomAD database, including 10,742 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 0.36 (10742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 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: 0.363 AC: 55223 AN: 151988 Hom.: 10745 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.363 AC: 55234 AN: 152106 Hom.: 10742 Cov.: 32 AF XY: 0.360 AC XY: 26777 AN XY: 74350

African (AFR) AF: 0.263 AC: 10899 AN: 41498

American (AMR) AF: 0.358 AC: 5466 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3468

East Asian (EAS) AF: 0.149 AC: 774 AN: 5184

South Asian (SAS) AF: 0.172 AC: 829 AN: 4814

European-Finnish (FIN) AF: 0.439 AC: 4633 AN: 10544

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29949 AN: 67996

Other (OTH) AF: 0.375 AC: 791 AN: 2112

Alfa AF: 0.410 Hom.: 21802

Bravo AF: 0.357

Asia WGS AF: 0.176 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.74
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4942925; hg19: chr13-33381244;