13-20335909-T-C

Variant names:

• chr13-20335909-T-C
• rs12868032

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 0.474 in 152,098 control chromosomes in the GnomAD database, including 18,556 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 0.47 (18556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72076 AN: 151982 Hom.: 18548 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.474 AC: 72122 AN: 152098 Hom.: 18556 Cov.: 32 AF XY: 0.472 AC XY: 35120 AN XY: 74360

African (AFR) AF: 0.283 AC: 11749 AN: 41516

American (AMR) AF: 0.559 AC: 8547 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1330 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1395 AN: 5176

South Asian (SAS) AF: 0.540 AC: 2603 AN: 4818

European-Finnish (FIN) AF: 0.547 AC: 5771 AN: 10558

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39038 AN: 67968

Other (OTH) AF: 0.478 AC: 1004 AN: 2100

Alfa AF: 0.539 Hom.: 63751

Bravo AF: 0.464

Asia WGS AF: 0.473 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.29
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs12868032; hg19: chr13-20910048;