rs1827253

Positions:

• chr15-22305519-T-C

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00 AC: 34859 AN: 121938 Hom.: 465 Cov.: 28 FAILED QC

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

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.265

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1827253; hg19: chr15-22593470;