rs4778495

chr15-28425889-C-Gchr15-28425889-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 0.29 (786 hom., cov: 3)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

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: 8278 AN: 29006 Hom.: 778 Cov.: 3 FAILED QC

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.277

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: 0.286 AC: 8316 AN: 29102 Hom.: 786 Cov.: 3 AF XY: 0.291 AC XY: 4001 AN XY: 13746

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.300

Alfa AF: 0.0299 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.60
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4778495; hg19: chr15-28671035; COSMIC: COSV74011821;