13-42996751-A-C

Variant names:

• chr13-42996751-A-C
• rs9533338

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0289 in 152,292 control chromosomes in the GnomAD database, including 83 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 0.029 (83 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0289 (4397/152292) while in subpopulation NFE AF = 0.0415 (2825/68012). AF 95% confidence interval is 0.0403. There are 83 homozygotes in GnomAd4. There are 2181 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 83 gene

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: 0.0289 AC: 4397 AN: 152174 Hom.: 83 Cov.: 33

Gnomad AFR AF: 0.00646

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0425

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0289 AC: 4397 AN: 152292 Hom.: 83 Cov.: 33 AF XY: 0.0293 AC XY: 2181 AN XY: 74464

African (AFR) AF: 0.00645 AC: 268 AN: 41578

American (AMR) AF: 0.0360 AC: 551 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5190

South Asian (SAS) AF: 0.0265 AC: 128 AN: 4826

European-Finnish (FIN) AF: 0.0425 AC: 450 AN: 10590

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0415 AC: 2825 AN: 68012

Other (OTH) AF: 0.0312 AC: 66 AN: 2116

Alfa AF: 0.0349 Hom.: 162

Bravo AF: 0.0269

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.14
DANN	Benign	0.53
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs9533338; hg19: chr13-43570887;