chr19-19551411-C-T

Variant names:

• chr19-19551411-C-T
• rs17216525

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 0.0648 in 152,214 control chromosomes in the GnomAD database, including 351 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 0.065 (351 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 70 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0647 AC: 9837 AN: 152096 Hom.: 345 Cov.: 33

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0778

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0648 AC: 9858 AN: 152214 Hom.: 351 Cov.: 33 AF XY: 0.0655 AC XY: 4877 AN XY: 74420

African (AFR) AF: 0.0364 AC: 1512 AN: 41538

American (AMR) AF: 0.0581 AC: 889 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0482 AC: 167 AN: 3468

East Asian (EAS) AF: 0.0912 AC: 472 AN: 5174

South Asian (SAS) AF: 0.125 AC: 602 AN: 4822

European-Finnish (FIN) AF: 0.0613 AC: 649 AN: 10590

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0779 AC: 5295 AN: 68014

Other (OTH) AF: 0.0695 AC: 147 AN: 2114

Alfa AF: 0.0760 Hom.: 1513

Bravo AF: 0.0621

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs17216525; hg19: chr19-19662220;