rs891696485

chr19-10381501-A-Cchr19-10381501-A-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 0.00085 (0 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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: 92 AN: 108512 Hom.: 0 Cov.: 29 FAILED QC

Gnomad AFR AF: 0.000787

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000716

Gnomad ASJ AF: 0.00223

Gnomad EAS AF: 0.000532

Gnomad SAS AF: 0.00117

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000651

Gnomad OTH AF: 0.000651

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: 0.000848 AC: 92 AN: 108502 Hom.: 0 Cov.: 29 AF XY: 0.000912 AC XY: 47 AN XY: 51558

Gnomad4 AFR AF: 0.000786

Gnomad4 AMR AF: 0.000715

Gnomad4 ASJ AF: 0.00223

Gnomad4 EAS AF: 0.000533

Gnomad4 SAS AF: 0.00118

Gnomad4 FIN AF: 0.00292

Gnomad4 NFE AF: 0.000652

Gnomad4 OTH AF: 0.000648

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.5
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: rs891696485; hg19: chr19-10492177;