rs17216525

Variant names:

• chr19-19551411-C-T
• rs17216525

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 0.0648 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0647 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

Gnomad4 AFR AF: 0.0364

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.0912

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0613

Gnomad4 NFE AF: 0.0779

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0769 Hom.: 596

Bravo AF: 0.0621

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17216525; hg19: chr19-19662220;