13-113121343-G-C

Position:

• chr13-113121343-G-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 68 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113121343G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0191

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.00521

Gnomad4 SAS AF: 0.00974

Gnomad4 FIN AF: 0.0341

Gnomad4 NFE AF: 0.0400

Gnomad4 OTH AF: 0.0218

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093268; hg19: chr13-113775657;