Genetic Variant ENSG00000234378:n.352C>T (chr2-20135948-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000849275.1(ENSG00000234378):n.352C>T 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 0.434 in 151,948 control chromosomes in the GnomAD database, including 16,051 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 0.43 ( 16051 hom., cov: 30)

Consequence

ENSG00000234378
ENST00000849275.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.517

Publications

8 publications found

Variant links:

Genes affected

ENSG00000234378 (HGNC:):

ENSG00000234378 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000234378	ENST00000849275.1 link	n.352C>T	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000234378	ENST00000849271.1 link	n.140+147C>T	intron_variant	Intron 2 of 2
ENSG00000234378	ENST00000849272.1 link	n.249+147C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.434

AC:

65857

AN:

151830

Hom.:

16000

Cov.:

show subpopulations

Gnomad AFR

AF:

0.603

Gnomad AMI

AF:

0.409

Gnomad AMR

AF:

0.455

Gnomad ASJ

AF:

0.325

Gnomad EAS

AF:

0.811

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.290

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.401

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

GnomAD4 genome

AF:

0.434

AC:

65980

AN:

151948

Hom.:

16051

Cov.:

AF XY:

0.444

AC XY:

32976

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.603

AC:

24985

AN:

41414

American (AMR)

AF:

0.456

AC:

6968

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.325

AC:

1126

AN:

3466

East Asian (EAS)

AF:

0.811

AC:

4191

AN:

5166

South Asian (SAS)

AF:

0.569

AC:

2736

AN:

4808

European-Finnish (FIN)

AF:

0.380

AC:

4014

AN:

10564

Middle Eastern (MID)

AF:

0.295

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.304

AC:

20646

AN:

67950

Other (OTH)

AF:

0.407

AC:

857

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1724

3448

5172

6896

8620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

602

1204

1806

2408

3010

<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:

0.344

Hom.:

41065

Bravo

AF:

0.447

Asia WGS

AF:

0.677

AC:

2351

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

0.54

(source)

DANN

Benign

0.64

PhyloP100

-0.52

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