Genetic Variant ENST00000623093.1:n.1497A>G (chr18-12280923-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000623093.1(ENSG00000280302):n.1497A>G 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 0.353 in 152,124 control chromosomes in the GnomAD database, including 9,632 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 0.35 ( 9628 hom., cov: 32)

Exomes 𝑓: 0.35 ( 4 hom. )

Consequence

ENSG00000280302
ENST00000623093.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.87

Publications

3 publications found

Variant links:

Genes affected

ENSG00000280302 (HGNC:):

ENSG00000280302 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=-1.02).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000280302	ENST00000623093.1 link	n.1497A>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000267069	ENST00000772914.1 link	n.105+1849A>G	intron_variant	Intron 1 of 1
ENSG00000267069	ENST00000772915.1 link	n.334+1217A>G	intron_variant	Intron 1 of 1
ENSG00000267069	ENST00000772916.1 link	n.280+1217A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

53671

AN:

151932

Hom.:

9616

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.272

Gnomad SAS

AF:

0.434

Gnomad FIN

AF:

0.397

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.369

GnomAD4 exome

AF:

0.351

AC:

AN:

Hom.:

Cov.:

AF XY:

0.353

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

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:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.353

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

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:

0.353

AC:

53714

AN:

152050

Hom.:

9628

Cov.:

AF XY:

0.357

AC XY:

26513

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.295

AC:

12221

AN:

41472

American (AMR)

AF:

0.382

AC:

5835

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.351

AC:

1218

AN:

3470

East Asian (EAS)

AF:

0.272

AC:

1407

AN:

5170

South Asian (SAS)

AF:

0.436

AC:

2100

AN:

4822

European-Finnish (FIN)

AF:

0.397

AC:

4191

AN:

10560

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.375

AC:

25501

AN:

67956

Other (OTH)

AF:

0.371

AC:

784

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1794

3589

5383

7178

8972

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<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:

0.361

Hom.:

18793

Bravo

AF:

0.345

Asia WGS

AF:

0.376

AC:

1308

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.16

(source)

DANN

Benign

0.31

PhyloP100

-4.9

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