19-17848706-C-T

Position:

• chr19-17848706-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 0.45 in 151,934 control chromosomes in the GnomAD database, including 18,715 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 0.45 (18715 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17848706C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68258 AN: 151816 Hom.: 18672 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.450 AC: 68356 AN: 151934 Hom.: 18715 Cov.: 31 AF XY: 0.446 AC XY: 33114 AN XY: 74264

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.437

Alfa AF: 0.374 Hom.: 1567

Bravo AF: 0.479

Asia WGS AF: 0.389 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6512226; hg19: chr19-17959515;