13-113121343-G-C

Variant names:

• chr13-113121343-G-C
• rs3093268

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 0.027 in 152,366 control chromosomes in the GnomAD database, including 68 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 0.027 (68 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.027 (4110/152366) while in subpopulation NFE AF = 0.04 (2719/68030). AF 95% confidence interval is 0.0387. There are 68 homozygotes in GnomAd4. There are 2030 alleles in the male GnomAd4 subpopulation. Median coverage is 34. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 68 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: 0.0270 AC: 4106 AN: 152248 Hom.: 68 Cov.: 34

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0191

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.00520

Gnomad SAS AF: 0.00932

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0400

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0270 AC: 4110 AN: 152366 Hom.: 68 Cov.: 34 AF XY: 0.0272 AC XY: 2030 AN XY: 74500

African (AFR) AF: 0.0112 AC: 466 AN: 41604

American (AMR) AF: 0.0191 AC: 292 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3470

East Asian (EAS) AF: 0.00521 AC: 27 AN: 5182

South Asian (SAS) AF: 0.00974 AC: 47 AN: 4826

European-Finnish (FIN) AF: 0.0341 AC: 362 AN: 10624

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0400 AC: 2719 AN: 68030

Other (OTH) AF: 0.0218 AC: 46 AN: 2114

Alfa AF: 0.0225 Hom.: 8

Bravo AF: 0.0252

Asia WGS AF: 0.0150 AC: 53 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	0.12
DANN	Benign	0.39
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs3093268; hg19: chr13-113775657;