rs4778495

Variant names:

• chr15-28425889-C-G
• rs4778495

Your query was ambiguous. Multiple possible variants found:

• chr15-28425889-C-G
• chr15-28425889-C-T

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).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4778495;

hg19: chr15-28671035;

COSMIC: COSV74011821;