rs2194189

Positions:

• chr16-15205360-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.056 (355 hom., cov: 27)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00 AC: 8134 AN: 146414 Hom.: 355 Cov.: 27 FAILED QC

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.0200

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0117

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0776

Gnomad MID AF: 0.0260

Gnomad NFE AF: 0.0513

Gnomad OTH AF: 0.0494

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0556 AC: 8144 AN: 146534 Hom.: 355 Cov.: 27 AF XY: 0.0574 AC XY: 4102 AN XY: 71474

Gnomad4 AFR AF: 0.0382

Gnomad4 AMR AF: 0.0813

Gnomad4 ASJ AF: 0.0117

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.0681

Gnomad4 FIN AF: 0.0776

Gnomad4 NFE AF: 0.0513

Gnomad4 OTH AF: 0.0504

Alfa AF: 0.0762 Hom.: 59

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2194189; hg19: chr16-15299217;