19-17853069-T-G

Position:

• chr19-17853069-T-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 0.182 in 152,118 control chromosomes in the GnomAD database, including 2,594 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 0.18 (2594 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17853069T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27676 AN: 152000 Hom.: 2592 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.182 AC: 27685 AN: 152118 Hom.: 2594 Cov.: 31 AF XY: 0.182 AC XY: 13509 AN XY: 74390

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0456

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.190

Alfa AF: 0.189 Hom.: 3914

Bravo AF: 0.187

Asia WGS AF: 0.108 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.87
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7245564; hg19: chr19-17963878;