rs1827253

Variant names:

• chr15-22305519-T-C
• rs1827253

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 (466 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• 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=-0.91).

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: 0.286 AC: 34859 AN: 121938 Hom.: 465 Cov.: 28

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.264

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: 0.286 AC: 34896 AN: 122014 Hom.: 466 Cov.: 28 AF XY: 0.287 AC XY: 17041 AN XY: 59352

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.400 AC: 13491 AN: 33702

American (AMR) AF: 0.255 AC: 3137 AN: 12294

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 762 AN: 2880

East Asian (EAS) AF: 0.165 AC: 734 AN: 4454

South Asian (SAS) AF: 0.239 AC: 923 AN: 3856

European-Finnish (FIN) AF: 0.268 AC: 2167 AN: 8084

Middle Eastern (MID) AF: 0.278 AC: 69 AN: 248

European-Non Finnish (NFE) AF: 0.240 AC: 12942 AN: 54016

Other (OTH) AF: 0.265 AC: 455 AN: 1716

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.268 Hom.: 48

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.43
PhyloP100		-2.0

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: rs1827253;

hg19: chr15-22593470;