Genetic Variant ENSG00000293318:n.361-4254T>C (chr2-57760458-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 ENST00000605503.2(ENSG00000293318):n.361-4254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,094 control chromosomes in the GnomAD database, including 12,224 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 0.39 ( 12224 hom., cov: 32)

Consequence

ENSG00000293318
ENST00000605503.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.499

Publications

53 publications found

Variant links:

Genes affected

ENSG00000293318 (HGNC:):

ENSG00000293318 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 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
ENSG00000293318	ENST00000605503.2 link	n.361-4254T>C	intron_variant	Intron 1 of 1	4
ENSG00000293611	ENST00000715879.1 link	n.499-13737A>G	intron_variant	Intron 5 of 5
ENSG00000293611	ENST00000715880.1 link	n.162-13737A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.385

AC:

58586

AN:

151976

Hom.:

12224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.555

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.524

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.396

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.473

Gnomad OTH

AF:

0.420

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

GnomAD4 genome

AF:

0.385

AC:

58596

AN:

152094

Hom.:

12224

Cov.:

AF XY:

0.381

AC XY:

28331

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.217

AC:

9017

AN:

41500

American (AMR)

AF:

0.396

AC:

6046

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.524

AC:

1817

AN:

3470

East Asian (EAS)

AF:

0.386

AC:

1998

AN:

5178

South Asian (SAS)

AF:

0.397

AC:

1913

AN:

4816

European-Finnish (FIN)

AF:

0.391

AC:

4140

AN:

10576

Middle Eastern (MID)

AF:

0.466

AC:

137

AN:

294

European-Non Finnish (NFE)

AF:

0.473

AC:

32147

AN:

67970

Other (OTH)

AF:

0.414

AC:

876

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1746

3492

5239

6985

8731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

574

1148

1722

2296

2870

<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:

0.444

Hom.:

32690

Bravo

AF:

0.379

Asia WGS

AF:

0.362

AC:

1260

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.9

(source)

DANN

Benign

0.46

PhyloP100

0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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