rs9536579

Positions:

• chr13-53995230-G-A

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 0.213 in 152,028 control chromosomes in the GnomAD database, including 3,828 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 (3828 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53995230G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00458	ENST00000706980.1	n.465-36800C>T		intron_variant
LINC00458	ENST00000706981.1	n.571-10412C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32397 AN: 151910 Hom.: 3820 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.213 AC: 32417 AN: 152028 Hom.: 3828 Cov.: 32 AF XY: 0.213 AC XY: 15838 AN XY: 74300

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.231

Alfa AF: 0.224 Hom.: 5522

Bravo AF: 0.212

Asia WGS AF: 0.381 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.82
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9536579; hg19: chr13-54569365;