Genetic Variant ENSG00000266573:n.562-33407C>T (chr18-24876381-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 ENST00000577354.6(ENSG00000266573):n.562-33407C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 152,146 control chromosomes in the GnomAD database, including 1,334 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 0.083 ( 1334 hom., cov: 33)

Consequence

ENSG00000266573
ENST00000577354.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.78

Publications

1 publications found

Variant links:

Genes affected

ENSG00000266573 (HGNC:):

ENSG00000266573 links:

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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 = 0.369 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
ENSG00000266573	ENST00000577354.6 link	n.562-33407C>T	intron_variant	Intron 3 of 3	4
ENSG00000266573	ENST00000582650.5 link	n.236-51457C>T	intron_variant	Intron 2 of 3	4
ENSG00000266573	ENST00000654065.1 link	n.227-59601C>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.0833

AC:

12663

AN:

152028

Hom.:

1332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.0161

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00387

Gnomad OTH

AF:

0.0584

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0834

AC:

12684

AN:

152146

Hom.:

1334

Cov.:

AF XY:

0.0874

AC XY:

6498

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.192

AC:

7949

AN:

41506

American (AMR)

AF:

0.103

AC:

1577

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3472

East Asian (EAS)

AF:

0.383

AC:

1967

AN:

5140

South Asian (SAS)

AF:

0.128

AC:

618

AN:

4816

European-Finnish (FIN)

AF:

0.0161

AC:

171

AN:

10600

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00387

AC:

263

AN:

68012

Other (OTH)

AF:

0.0592

AC:

125

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

517

1034

1551

2068

2585

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<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:

0.0551

Hom.:

119

Bravo

AF:

0.0952

Asia WGS

AF:

0.196

AC:

682

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

0.018

(source)

DANN

Benign

0.64

PhyloP100

-2.8

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