rs17660300

Variant names:

• chr19-46227203-C-T
• rs17660300

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 0.4 in 151,728 control chromosomes in the GnomAD database, including 12,962 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 0.40 (12962 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 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: 0.401 AC: 60751 AN: 151610 Hom.: 12970 Cov.: 30

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.400 AC: 60753 AN: 151728 Hom.: 12962 Cov.: 30 AF XY: 0.395 AC XY: 29242 AN XY: 74120

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.423

Alfa AF: 0.419 Hom.: 1754

Bravo AF: 0.386

Asia WGS AF: 0.358 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17660300; hg19: chr19-46730460;