19-17848706-C-T

Variant names:

• chr19-17848706-C-T
• rs6512226

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.778 AC: 32224 AN: 41432

American (AMR) AF: 0.435 AC: 6639 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2029 AN: 5152

South Asian (SAS) AF: 0.341 AC: 1640 AN: 4814

European-Finnish (FIN) AF: 0.243 AC: 2573 AN: 10568

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20712 AN: 67926

Other (OTH) AF: 0.437 AC: 921 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs6512226; hg19: chr19-17959515;