dbSNP rs10189532: ENSG00000237844:n.380-12408C>T (chr2-163762315-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The ENST00000429636.1(ENSG00000237844):n.380-12408C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,918 control chromosomes in the GnomAD database, including 1,766 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 0.14 ( 1766 hom., cov: 32)

Consequence

ENSG00000237844
ENST00000429636.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.193

Publications

2 publications found

Variant links:

Genes affected

ENSG00000237844 (HGNC:58942):

ENSG00000237844 links:

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new If you want to explore the variant's impact on the transcript ENST00000429636.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.26).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429636.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237844	ENST00000429636.1	TSL:3	n.380-12408C>T		intron	N/A
	ENSG00000237844	ENST00000666867.1		n.455-12408C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21357

AN:

151800

Hom.:

1761

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.0551

Gnomad EAS

AF:

0.0126

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.131

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

GnomAD4 genome

AF:

0.141

AC:

21385

AN:

151918

Hom.:

1766

Cov.:

AF XY:

0.139

AC XY:

10351

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.229

AC:

9484

AN:

41422

American (AMR)

AF:

0.115

AC:

1752

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.0551

AC:

191

AN:

3468

East Asian (EAS)

AF:

0.0126

AC:

AN:

5152

South Asian (SAS)

AF:

0.111

AC:

533

AN:

4818

European-Finnish (FIN)

AF:

0.109

AC:

1154

AN:

10582

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7781

AN:

67922

Other (OTH)

AF:

0.129

AC:

273

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

919

1838

2757

3676

4595

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.132

Hom.:

1125

Bravo

AF:

0.143

Asia WGS

AF:

0.0880

AC:

307

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

(source)

DANN

Benign

0.57

PhyloP100

0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over