rs17660300

Variant names:

• chr19-46227203-C-T
• rs17660300

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 0.4 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.401 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

African (AFR) AF: 0.291 AC: 12047 AN: 41352

American (AMR) AF: 0.314 AC: 4787 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1991 AN: 3466

East Asian (EAS) AF: 0.331 AC: 1702 AN: 5140

South Asian (SAS) AF: 0.405 AC: 1948 AN: 4804

European-Finnish (FIN) AF: 0.398 AC: 4179 AN: 10500

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.481 AC: 32659 AN: 67910

Other (OTH) AF: 0.423 AC: 890 AN: 2102

Alfa AF: 0.414 Hom.: 1790

Bravo AF: 0.386

Asia WGS AF: 0.358 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs17660300; hg19: chr19-46730460;