Genetic Variant ENSG00000290466:n.409+8497G>A (chr1-48119411-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000452503.1(ENSG00000290466):n.409+8497G>A variant causes a intron 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 0.0 ( 0 hom., cov: 31)

Failed GnomAD Quality Control

Consequence

ENSG00000290466
ENST00000452503.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550

Publications

2 publications found

Variant links:

Genes affected

ENSG00000290466 (HGNC:):

ENSG00000290466 links:

SKINT1L (HGNC:33993): (Skint1 like (pseudogene))

SKINT1L links:

LINC02794 (HGNC:54318): (long intergenic non-protein coding RNA 2794)

LINC02794 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
SKINT1L	NR_026749.2 link	n.1275+8497G>A	intron_variant	Intron 9 of 9
LINC02794	XR_007066068.1 link	n.3463+18559C>T	intron_variant	Intron 8 of 12
LINC02794	XR_007066069.1 link	n.3463+18559C>T	intron_variant	Intron 8 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000290466	ENST00000452503.1 link	n.409+8497G>A	intron_variant	Intron 4 of 4	2
ENSG00000290466	ENST00000604015.1 link	n.41+8497G>A	intron_variant	Intron 1 of 1	4
ENSG00000290466	ENST00000706231.2 link	n.1048-17461G>A	intron_variant	Intron 7 of 7
ENSG00000290466	ENST00000788051.1 link	n.720+8497G>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

151422

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

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: AC0

AF:

0.00

AC:

AN:

151422

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

73954

African (AFR)

AF:

0.00

AC:

AN:

40798

American (AMR)

AF:

0.00

AC:

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5188

South Asian (SAS)

AF:

0.00

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10584

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68018

Other (OTH)

AF:

0.00

AC:

AN:

2084

Alfa

AF:

0.00

Hom.:

8269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.077

(source)

DANN

Benign

0.71

PhyloP100

0.055

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over