Genetic Variant ENSG00000228037:n.462C>T (chr1-2581777-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 ENST00000829924.1(ENSG00000228037):n.462C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,020 control chromosomes in the GnomAD database, including 26,883 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 0.58 ( 26881 hom., cov: 32)

Exomes 𝑓: 0.42 ( 2 hom. )

Consequence

ENSG00000228037
ENST00000829924.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.202

Publications

60 publications found

Variant links:

Genes affected

ENSG00000228037 (HGNC:):

ENSG00000228037 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100996583	NR_121638.1 link	n.162+127C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228037	ENST00000829924.1 link	n.462C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000228037	ENST00000424215.2 link	n.945+127C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87682

AN:

151842

Hom.:

26841

Cov.:

show subpopulations

Gnomad AFR

AF:

0.795

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.546

Gnomad ASJ

AF:

0.452

Gnomad EAS

AF:

0.540

Gnomad SAS

AF:

0.659

Gnomad FIN

AF:

0.500

Gnomad MID

AF:

0.548

Gnomad NFE

AF:

0.473

Gnomad OTH

AF:

0.549

GnomAD4 exome

AF:

0.417

AC:

AN:

Hom.:

AF XY:

0.344

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)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.389

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.421

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.446

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.578

AC:

87774

AN:

151960

Hom.:

26881

Cov.:

AF XY:

0.579

AC XY:

42971

AN XY:

74220

show subpopulations

African (AFR)

AF:

0.795

AC:

32955

AN:

41452

American (AMR)

AF:

0.546

AC:

8348

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.452

AC:

1568

AN:

3470

East Asian (EAS)

AF:

0.539

AC:

2784

AN:

5164

South Asian (SAS)

AF:

0.659

AC:

3180

AN:

4822

European-Finnish (FIN)

AF:

0.500

AC:

5259

AN:

10524

Middle Eastern (MID)

AF:

0.531

AC:

155

AN:

292

European-Non Finnish (NFE)

AF:

0.473

AC:

32103

AN:

67942

Other (OTH)

AF:

0.554

AC:

1165

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1753

3506

5258

7011

8764

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

724

1448

2172

2896

3620

<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:

0.503

Hom.:

85725

Bravo

AF:

0.584

Asia WGS

AF:

0.680

AC:

2366

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.4

(source)

DANN

Benign

0.78

PhyloP100

0.20

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