chr15-28425889-C-G

Variant names:

• chr15-28425889-C-G
• rs4778495

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.285 AC: 8278 AN: 29006 Hom.: 778 Cov.: 3

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

African (AFR) AF: 0.223 AC: 4645 AN: 20852

American (AMR) AF: 0.409 AC: 938 AN: 2292

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 112 AN: 232

East Asian (EAS) AF: 0.569 AC: 911 AN: 1600

South Asian (SAS) AF: 0.515 AC: 351 AN: 682

European-Finnish (FIN) AF: 0.535 AC: 76 AN: 142

Middle Eastern (MID) AF: 0.365 AC: 19 AN: 52

European-Non Finnish (NFE) AF: 0.399 AC: 1120 AN: 2804

Other (OTH) AF: 0.300 AC: 114 AN: 380

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

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