13-57472128-C-G

Position:

• chr13-57472128-C-G

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 0.333 in 151,792 control chromosomes in the GnomAD database, including 8,822 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 0.33 (8822 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57472128C>G		intergenic_region
LOC105370217	XR_941983.1	n.577-14338G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50486 AN: 151674 Hom.: 8794 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.333 AC: 50558 AN: 151792 Hom.: 8822 Cov.: 31 AF XY: 0.340 AC XY: 25227 AN XY: 74170

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.294

Alfa AF: 0.230 Hom.: 540

Bravo AF: 0.331

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs986642; hg19: chr13-58046262;