chr5-53492371-G-A

Position:

• chr5-53492371-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 0.313 in 151,918 control chromosomes in the GnomAD database, including 7,492 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 0.31 (7492 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53492371G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47539 AN: 151802 Hom.: 7487 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.313 AC: 47585 AN: 151918 Hom.: 7492 Cov.: 31 AF XY: 0.315 AC XY: 23394 AN XY: 74228

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.327

Alfa AF: 0.324 Hom.: 15160

Bravo AF: 0.307

Asia WGS AF: 0.245 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12521153; hg19: chr5-52788201;