Genetic Variant ENSG00000267675:n.58T>C (chr18-58416822-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 ENST00000585470.1(ENSG00000267675):n.58T>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 0.81 in 152,100 control chromosomes in the GnomAD database, including 50,006 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 0.81 ( 50006 hom., cov: 34)

Exomes 𝑓: 0.77 ( 34 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000267675
ENST00000585470.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05

Publications

15 publications found

Variant links:

Genes affected

ENSG00000267675 (HGNC:):

ENSG00000267675 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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
ENSG00000267675	ENST00000585470.1 link	n.58T>C	non_coding_transcript_exon_variant	Exon 1 of 2	5
ENSG00000300063	ENST00000768485.1 link	n.157+2310A>G	intron_variant	Intron 2 of 3
ENSG00000300063	ENST00000768488.1 link	n.297+2310A>G	intron_variant	Intron 2 of 3
ENSG00000300063	ENST00000768489.1 link	n.313+2310A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.810

AC:

123112

AN:

151980

Hom.:

49955

Cov.:

show subpopulations

Gnomad AFR

AF:

0.837

Gnomad AMI

AF:

0.831

Gnomad AMR

AF:

0.822

Gnomad ASJ

AF:

0.760

Gnomad EAS

AF:

0.856

Gnomad SAS

AF:

0.800

Gnomad FIN

AF:

0.768

Gnomad MID

AF:

0.732

Gnomad NFE

AF:

0.798

Gnomad OTH

AF:

0.797

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.767

AC:

AN:

116

Hom.:

Cov.:

AF XY:

0.756

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.833

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.761

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.810

AC:

123223

AN:

152100

Hom.:

50006

Cov.:

AF XY:

0.807

AC XY:

60051

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.837

AC:

34698

AN:

41470

American (AMR)

AF:

0.822

AC:

12571

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.760

AC:

2638

AN:

3470

East Asian (EAS)

AF:

0.856

AC:

4430

AN:

5178

South Asian (SAS)

AF:

0.801

AC:

3862

AN:

4822

European-Finnish (FIN)

AF:

0.768

AC:

8118

AN:

10566

Middle Eastern (MID)

AF:

0.729

AC:

213

AN:

292

European-Non Finnish (NFE)

AF:

0.798

AC:

54257

AN:

67988

Other (OTH)

AF:

0.794

AC:

1680

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1203

2406

3608

4811

6014

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

878

1756

2634

3512

4390

<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:

0.821

Hom.:

20263

Bravo

AF:

0.814

Asia WGS

AF:

0.826

AC:

2871

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.2

(source)

DANN

Benign

0.45

PhyloP100

-1.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over