Genetic Variant ENST00000452494.2:n.257+353C>T (chr10-99527557-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000452494.2(ENSG00000228778):n.257+353C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,218 control chromosomes in the GnomAD database, including 7,159 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 0.29 ( 7156 hom., cov: 33)

Exomes 𝑓: 0.19 ( 3 hom. )

Consequence

ENSG00000228778
ENST00000452494.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.118

Variant links:

Genes affected

ENSG00000228778 (HGNC:):

ENSG00000228778 links:

LINC01475 (HGNC:51113): (long intergenic non-protein coding RNA 1475)

LINC01475 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01475	NR_120618.1 link	n.577+249G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000228778	ENST00000452494.2 link	n.257+353C>T	intron_variant	Intron 1 of 1	1
LINC01475	ENST00000548010.1 link	n.577+249G>A	intron_variant	Intron 3 of 4	1
LINC01475	ENST00000552096.5 link	n.-114G>A	upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43386

AN:

151988

Hom.:

7141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.260

GnomAD4 exome

AF:

0.188

AC:

AN:

112

Hom.:

AF XY:

0.209

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.0833

Gnomad4 NFE exome

AF:

0.189

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.286

AC:

43445

AN:

152106

Hom.:

7156

Cov.:

AF XY:

0.281

AC XY:

20895

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.430

Gnomad4 AMR

AF:

0.262

Gnomad4 ASJ

AF:

0.250

Gnomad4 EAS

AF:

0.115

Gnomad4 SAS

AF:

0.415

Gnomad4 FIN

AF:

0.134

Gnomad4 NFE

AF:

0.234

Gnomad4 OTH

AF:

0.260

Alfa

AF:

0.268

Hom.:

1295

Bravo

AF:

0.299

Asia WGS

AF:

0.309

AC:

1075

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.1

DANN

Benign

0.82

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