19-5524710-C-T

Position:

• chr19-5524710-C-T

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 0.137 in 151,970 control chromosomes in the GnomAD database, including 1,736 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 0.14 (1736 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5524710C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20838 AN: 151852 Hom.: 1735 Cov.: 31

Gnomad AFR AF: 0.0356

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.137 AC: 20846 AN: 151970 Hom.: 1736 Cov.: 31 AF XY: 0.136 AC XY: 10112 AN XY: 74284

Gnomad4 AFR AF: 0.0355

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.143

Alfa AF: 0.176 Hom.: 2463

Bravo AF: 0.133

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17271855; hg19: chr19-5524721;