13-20921370-G-C

Position:

• chr13-20921370-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.207 in 152,024 control chromosomes in the GnomAD database, including 3,512 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 0.21 (3512 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20921370G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31458 AN: 151906 Hom.: 3513 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.207 AC: 31468 AN: 152024 Hom.: 3512 Cov.: 33 AF XY: 0.201 AC XY: 14915 AN XY: 74308

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0975

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.224

Alfa AF: 0.134 Hom.: 242

Bravo AF: 0.209

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9579975; hg19: chr13-21495509;