rs4105144

chr19-40852719-T-C

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 0.44 (3619 hom., cov: 39)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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: 66450 AN: 150086 Hom.: 3617 Cov.: 39 FAILED QC

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.443

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: InbreedingCoeff AF: 0.443 AC: 66479 AN: 150196 Hom.: 3619 Cov.: 39 AF XY: 0.442 AC XY: 32380 AN XY: 73308

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.442

Alfa AF: 0.458 Hom.: 538

Asia WGS AF: 0.395 AC: 1360 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.11
Dann	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4105144; hg19: chr19-41358624;