Genetic Variant ENSG00000237844:n.197-138275C>G (chr2-164088534-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000429636.1(ENSG00000237844):n.197-138275C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,062 control chromosomes in the GnomAD database, including 2,646 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 0.17 ( 2646 hom., cov: 31)

Consequence

ENSG00000237844
ENST00000429636.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.444

Publications

11 publications found

Variant links:

Genes affected

ENSG00000237844 (HGNC:):

ENSG00000237844 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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
ENSG00000237844	ENST00000429636.1 link	n.197-138275C>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.175

AC:

26599

AN:

151944

Hom.:

2642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.292

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.412

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.197

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

GnomAD4 genome

AF:

0.175

AC:

26608

AN:

152062

Hom.:

2646

Cov.:

AF XY:

0.173

AC XY:

12875

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.149

AC:

6198

AN:

41510

American (AMR)

AF:

0.191

AC:

2916

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.207

AC:

720

AN:

3470

East Asian (EAS)

AF:

0.412

AC:

2115

AN:

5130

South Asian (SAS)

AF:

0.224

AC:

1076

AN:

4814

European-Finnish (FIN)

AF:

0.108

AC:

1140

AN:

10602

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.172

AC:

11688

AN:

67974

Other (OTH)

AF:

0.198

AC:

418

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1086

2172

3259

4345

5431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<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:

0.0598

Hom.:

Bravo

AF:

0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.43

(source)

DANN

Benign

0.50

PhyloP100

-0.44

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