rs3119939

chr13-63064196-T-C

Variant summary

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

The ENST00000658907.1(ENSG00000273550):n.82+29164T>C 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 0.27 (13 hom., cov: 72)
  • Failed GnomAD Quality Control
• Consequence: ENST00000658907.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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+29164T>C		intron_variant, non_coding_transcript_variant
	ENST00000618134.1	n.177+11788T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 34145 AN: 127808 Hom.: 13 Cov.: 72 FAILED QC

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0180

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.267

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: 0.267 AC: 34143 AN: 127924 Hom.: 13 Cov.: 72 AF XY: 0.261 AC XY: 16323 AN XY: 62530

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.262

Alfa AF: 0.439 Hom.: 21116

Asia WGS AF: 0.207 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	5.6
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3119939; hg19: chr13-63638329;