Genetic Variant ENSG00000237843:n.269-3880T>C (chr2-204503735-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 ENST00000456384.1(ENSG00000237843):n.269-3880T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 152,212 control chromosomes in the GnomAD database, including 377 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 0.054 ( 377 hom., cov: 33)

Consequence

ENSG00000237843
ENST00000456384.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.224

Publications

3 publications found

Variant links:

Genes affected

ENSG00000237843 (HGNC:):

ENSG00000237843 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237843	ENST00000456384.1 link	n.269-3880T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8229

AN:

152092

Hom.:

374

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0621

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.0306

Gnomad ASJ

AF:

0.0485

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.0988

Gnomad FIN

AF:

0.0344

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0384

Gnomad OTH

AF:

0.0507

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

GnomAD4 genome

AF:

0.0542

AC:

8248

AN:

152212

Hom.:

377

Cov.:

AF XY:

0.0552

AC XY:

4108

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0622

AC:

2584

AN:

41538

American (AMR)

AF:

0.0308

AC:

471

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0485

AC:

168

AN:

3466

East Asian (EAS)

AF:

0.276

AC:

1426

AN:

5166

South Asian (SAS)

AF:

0.0980

AC:

472

AN:

4814

European-Finnish (FIN)

AF:

0.0344

AC:

365

AN:

10614

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0384

AC:

2614

AN:

68016

Other (OTH)

AF:

0.0545

AC:

115

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

380

759

1139

1518

1898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0465

Hom.:

524

Bravo

AF:

0.0539

Asia WGS

AF:

0.219

AC:

758

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.5

(source)

DANN

Benign

0.76

PhyloP100

0.22

Mutation Taster

=100/0

polymorphism

(source)

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