Genetic Variant ENSG00000237588:n.1841G>A (chr1-156689976-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 ENST00000441272.2(ENSG00000237588):n.1841G>A 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 0.699 in 152,174 control chromosomes in the GnomAD database, including 37,290 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 0.70 ( 37256 hom., cov: 31)

Exomes 𝑓: 0.71 ( 34 hom. )

Consequence

ENSG00000237588
ENST00000441272.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.386

Publications

12 publications found

Variant links:

Genes affected

ENSG00000237588 (HGNC:):

ENSG00000237588 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237588	ENST00000441272.2 link	n.1841G>A		non_coding_transcript_exon_variant	Exon 2 of 2	5
ENSG00000285570	ENST00000650347.1 link	n.149+152C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.699

AC:

106151

AN:

151920

Hom.:

37224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.751

Gnomad AMI

AF:

0.834

Gnomad AMR

AF:

0.649

Gnomad ASJ

AF:

0.724

Gnomad EAS

AF:

0.662

Gnomad SAS

AF:

0.726

Gnomad FIN

AF:

0.738

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.671

Gnomad OTH

AF:

0.666

GnomAD4 exome

AF:

0.706

AC:

AN:

136

Hom.:

Cov.:

AF XY:

0.693

AC XY:

AN XY:

114

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.739

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

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:

0.699

AC:

106234

AN:

152038

Hom.:

37256

Cov.:

AF XY:

0.700

AC XY:

52058

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.752

AC:

31180

AN:

41482

American (AMR)

AF:

0.648

AC:

9908

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.724

AC:

2512

AN:

3468

East Asian (EAS)

AF:

0.662

AC:

3393

AN:

5126

South Asian (SAS)

AF:

0.725

AC:

3501

AN:

4826

European-Finnish (FIN)

AF:

0.738

AC:

7825

AN:

10598

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.671

AC:

45568

AN:

67936

Other (OTH)

AF:

0.661

AC:

1396

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1641

3281

4922

6562

8203

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

826

1652

2478

3304

4130

<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:

0.679

Hom.:

143800

Bravo

AF:

0.698

Asia WGS

AF:

0.639

AC:

2220

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

8.0

(source)

DANN

Benign

0.38

PhyloP100

0.39

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