Variant chr15-93736606-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000554318.2(ENSG00000258631):n.325-24061T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,024 control chromosomes in the GnomAD database, including 19,224 homozygotes. 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 ( 19224 hom., cov: 33)

Consequence

ENSG00000258631
ENST00000554318.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147

Variant links:

Genes affected

ENSG00000258631 (HGNC:):

ENSG00000258631 links:

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

LINC01579 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107983974	XR_001751681.2 link	n.1033-24061T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000258631	ENST00000554318.2 link	n.325-24061T>C	intron_variant	3
LINC01579	ENST00000557481.6 link	n.1054-5255A>G	intron_variant	5
ENSG00000258631	ENST00000653322.1 link	n.173-24061T>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.499

AC:

75856

AN:

151908

Hom.:

19195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.515

Gnomad AMI

AF:

0.448

Gnomad AMR

AF:

0.537

Gnomad ASJ

AF:

0.537

Gnomad EAS

AF:

0.468

Gnomad SAS

AF:

0.668

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.469

Gnomad OTH

AF:

0.487

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.499

AC:

75933

AN:

152024

Hom.:

19224

Cov.:

AF XY:

0.507

AC XY:

37703

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.516

Gnomad4 AMR

AF:

0.538

Gnomad4 ASJ

AF:

0.537

Gnomad4 EAS

AF:

0.468

Gnomad4 SAS

AF:

0.669

Gnomad4 FIN

AF:

0.507

Gnomad4 NFE

AF:

0.469

Gnomad4 OTH

AF:

0.483

Alfa

AF:

0.473

Hom.:

2060

Bravo

AF:

0.496

Asia WGS

AF:

0.571

AC:

1986

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

4.1

DANN

Benign

0.46

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over