Genetic Variant ENSG00000228778: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.

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	ENST00000452494.3 link	n.1522+353C>T	intron_variant	Intron 1 of 1	1
LINC01475	ENST00000548010.2 link	n.654+249G>A	intron_variant	Intron 3 of 5	1
LINC01475	ENST00000795235.1 link	n.98G>A	non_coding_transcript_exon_variant	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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over