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).

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: 0.286 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 v4.3

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

Other links and lift over

dbSNP: rs1827253; hg19: chr15-22593470;