Genetic Variant ENST00000623027.1:n.1494T>C (chr22-27020862-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000623027.1(ENSG00000279440):n.1494T>C 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 0.858 in 151,982 control chromosomes in the GnomAD database, including 56,188 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 0.86 ( 56180 hom., cov: 29)

Exomes 𝑓: 0.94 ( 8 hom. )

Consequence

ENSG00000279440
ENST00000623027.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.13

Publications

9 publications found

Variant links:

Genes affected

ENSG00000279440 (HGNC:):

ENSG00000279440 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 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
ENSG00000279440	ENST00000623027.1 link	n.1494T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000308315	ENST00000833191.1 link	n.2015A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.858

AC:

130218

AN:

151846

Hom.:

56130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.940

Gnomad AMI

AF:

0.849

Gnomad AMR

AF:

0.794

Gnomad ASJ

AF:

0.832

Gnomad EAS

AF:

0.716

Gnomad SAS

AF:

0.793

Gnomad FIN

AF:

0.839

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.841

Gnomad OTH

AF:

0.864

GnomAD4 exome

AF:

0.944

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

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:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.917

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.725

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.858

AC:

130332

AN:

151964

Hom.:

56180

Cov.:

AF XY:

0.855

AC XY:

63509

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.940

AC:

38964

AN:

41444

American (AMR)

AF:

0.794

AC:

12138

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.832

AC:

2882

AN:

3466

East Asian (EAS)

AF:

0.715

AC:

3667

AN:

5130

South Asian (SAS)

AF:

0.793

AC:

3793

AN:

4782

European-Finnish (FIN)

AF:

0.839

AC:

8875

AN:

10578

Middle Eastern (MID)

AF:

0.884

AC:

260

AN:

294

European-Non Finnish (NFE)

AF:

0.841

AC:

57161

AN:

67976

Other (OTH)

AF:

0.864

AC:

1819

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

908

1817

2725

3634

4542

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<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:

0.850

Hom.:

75770

Bravo

AF:

0.856

Asia WGS

AF:

0.765

AC:

2661

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.27

(source)

DANN

Benign

0.45

PhyloP100

-2.1

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