Genetic Variant ENSG00000213981:n.389-1254T>G (chr2-170684313-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000428156.1(ENSG00000213981):n.389-1254T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,020 control chromosomes in the GnomAD database, including 10,752 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 0.37 ( 10752 hom., cov: 32)

Consequence

ENSG00000213981
ENST00000428156.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00200

Publications

18 publications found

Variant links:

Genes affected

ENSG00000213981 (HGNC:):

ENSG00000213981 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC100130256	NR_187617.1 link	n.145-1254T>G	intron_variant	Intron 1 of 14
LOC100130256	NR_187618.1 link	n.145-1254T>G	intron_variant	Intron 1 of 13
LOC100130256	NR_187619.1 link	n.145-1254T>G	intron_variant	Intron 1 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000213981	ENST00000428156.1 link	n.389-1254T>G		intron_variant	Intron 1 of 9	2

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56361

AN:

151902

Hom.:

10729

Cov.:

show subpopulations

Gnomad AFR

AF:

0.358

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.507

Gnomad ASJ

AF:

0.291

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.391

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.356

Gnomad OTH

AF:

0.369

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

GnomAD4 genome

AF:

0.371

AC:

56427

AN:

152020

Hom.:

10752

Cov.:

AF XY:

0.373

AC XY:

27702

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.358

AC:

14864

AN:

41488

American (AMR)

AF:

0.508

AC:

7749

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.291

AC:

1010

AN:

3468

East Asian (EAS)

AF:

0.285

AC:

1472

AN:

5166

South Asian (SAS)

AF:

0.390

AC:

1879

AN:

4822

European-Finnish (FIN)

AF:

0.386

AC:

4078

AN:

10554

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.356

AC:

24226

AN:

67956

Other (OTH)

AF:

0.370

AC:

779

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1817

3633

5450

7266

9083

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<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:

0.359

Hom.:

33964

Bravo

AF:

0.383

Asia WGS

AF:

0.357

AC:

1239

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

4.6

(source)

DANN

Benign

0.73

PhyloP100

0.0020

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