Genetic Variant ENSG00000266578:n.1202+1310T>C (chr18-3328748-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 ENST00000578787.3(ENSG00000266578):n.1202+1310T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,206 control chromosomes in the GnomAD database, including 3,288 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 0.21 ( 3288 hom., cov: 32)

Consequence

ENSG00000266578
ENST00000578787.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.111

Publications

5 publications found

Variant links:

Genes affected

ENSG00000266578 (HGNC:):

ENSG00000266578 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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.241 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
ENSG00000266578	ENST00000578787.3 link	n.1202+1310T>C	intron_variant	Intron 2 of 2	3
ENSG00000301728	ENST00000781104.1 link	n.61+1878A>G	intron_variant	Intron 1 of 2
ENSG00000301728	ENST00000781105.1 link	n.114+1878A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31204

AN:

152088

Hom.:

3281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.242

Gnomad AMR

AF:

0.248

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.207

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

GnomAD4 genome

AF:

0.205

AC:

31236

AN:

152206

Hom.:

3288

Cov.:

AF XY:

0.204

AC XY:

15185

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.179

AC:

7453

AN:

41534

American (AMR)

AF:

0.248

AC:

3790

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

689

AN:

3470

East Asian (EAS)

AF:

0.162

AC:

842

AN:

5186

South Asian (SAS)

AF:

0.202

AC:

974

AN:

4824

European-Finnish (FIN)

AF:

0.187

AC:

1982

AN:

10592

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.218

AC:

14792

AN:

67996

Other (OTH)

AF:

0.205

AC:

433

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1284

2568

3851

5135

6419

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.217

Hom.:

5672

Bravo

AF:

0.213

Asia WGS

AF:

0.167

AC:

577

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.55

PhyloP100

-0.11

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