19-17848706-C-T

Variant names:

• chr19-17848706-C-T
• rs6512226

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;