rs2651432

Positions:

• chr15-30323066-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 0.35 (242 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 48790 AN: 137832 Hom.: 241 Cov.: 29 FAILED QC

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.359

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;InbreedingCoeff AF: 0.354 AC: 48822 AN: 137940 Hom.: 242 Cov.: 29 AF XY: 0.355 AC XY: 23895 AN XY: 67336

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.360

Alfa AF: 0.366 Hom.: 56

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2651432; hg19: chr15-30615269;