rs9317284

chr13-63060217-G-Achr13-63060217-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000658907.1(ENSG00000273550):n.82+25185G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.50 (0 hom., cov: 60)
  • Failed GnomAD Quality Control
• Consequence: ENST00000658907.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658907.1	n.82+25185G>A		intron_variant, non_coding_transcript_variant
	ENST00000618134.1	n.177+7809G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 75638 AN: 151576 Hom.: 0 Cov.: 60 FAILED QC

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.499

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: 0.499 AC: 75698 AN: 151696 Hom.: 0 Cov.: 60 AF XY: 0.499 AC XY: 36977 AN XY: 74116

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.499

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.9
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317284; hg19: chr13-63634350;