Genetic Variant ENSG00000230805:n.1426G>A (chr14-101073047-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 ENST00000818881.1(ENSG00000230805):n.1426G>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 0.327 in 152,260 control chromosomes in the GnomAD database, including 9,043 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 0.33 ( 9042 hom., cov: 34)

Exomes 𝑓: 0.30 ( 1 hom. )

Consequence

ENSG00000230805
ENST00000818881.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0560

Publications

20 publications found

Variant links:

Genes affected

ENSG00000230805 (HGNC:):

ENSG00000230805 links:

MEG9 (HGNC:43874): (maternally expressed 9)

MEG9 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370670	NR_188195.1 link	n.1084-147G>A		intron_variant	Intron 4 of 4
MEG9	NR_047664.1 link	n.*110C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000230805	ENST00000818881.1 link	n.1426G>A	non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000230805	ENST00000448840.8 link	n.1107-147G>A	intron_variant	Intron 4 of 4	3
ENSG00000230805	ENST00000673125.1 link	n.571-147G>A	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49832

AN:

152112

Hom.:

9040

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.358

Gnomad ASJ

AF:

0.321

Gnomad EAS

AF:

0.459

Gnomad SAS

AF:

0.411

Gnomad FIN

AF:

0.509

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.373

Gnomad OTH

AF:

0.329

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

AF XY:

0.0833

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.429

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.300

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.546

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:

0.327

AC:

49845

AN:

152230

Hom.:

9042

Cov.:

AF XY:

0.335

AC XY:

24939

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.169

AC:

7018

AN:

41550

American (AMR)

AF:

0.359

AC:

5486

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

1116

AN:

3472

East Asian (EAS)

AF:

0.461

AC:

2378

AN:

5162

South Asian (SAS)

AF:

0.410

AC:

1981

AN:

4828

European-Finnish (FIN)

AF:

0.509

AC:

5395

AN:

10600

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.373

AC:

25377

AN:

67996

Other (OTH)

AF:

0.328

AC:

693

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1698

3396

5095

6793

8491

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.351

Hom.:

28683

Bravo

AF:

0.312

Asia WGS

AF:

0.429

AC:

1492

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.2

(source)

DANN

Benign

0.88

PhyloP100

0.056

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