Genetic Variant ENST00000452494.3:n.1522+353C>T (chr10-99527557-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000452494.3(ENSG00000228778):n.1522+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
ENST00000452494.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.118

Publications

5 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452494.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01475	NR_120618.1		n.577+249G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000228778	ENST00000452494.3	TSL:1	n.1522+353C>T	intron	N/A
LINC01475	ENST00000548010.2	TSL:1	n.654+249G>A	intron	N/A
LINC01475	ENST00000795235.1		n.98G>A	non_coding_transcript_exon	Exon 1 of 4

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

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.189

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.286

AC:

43445

AN:

152106

Hom.:

7156

Cov.:

AF XY:

0.281

AC XY:

20895

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.430

AC:

17843

AN:

41482

American (AMR)

AF:

0.262

AC:

4003

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

868

AN:

3468

East Asian (EAS)

AF:

0.115

AC:

593

AN:

5146

South Asian (SAS)

AF:

0.415

AC:

2002

AN:

4822

European-Finnish (FIN)

AF:

0.134

AC:

1420

AN:

10618

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.234

AC:

15879

AN:

67962

Other (OTH)

AF:

0.260

AC:

546

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1538

3076

4615

6153

7691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

442

884

1326

1768

2210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.272

Hom.:

1513

Bravo

AF:

0.299

Asia WGS

AF:

0.309

AC:

1075

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.1

(source)

DANN

Benign

0.82

PhyloP100

-0.12

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over