dbSNP rs10495886: ENSG00000298207:n.150-24032C>T (chr2-40861360-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000753888.1(ENSG00000298207):n.150-24032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 152,170 control chromosomes in the GnomAD database, including 577 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 0.038 ( 577 hom., cov: 32)

Consequence

ENSG00000298207
ENST00000753888.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.691

Publications

1 publications found

Variant links:

Genes affected

ENSG00000298207 (HGNC:):

ENSG00000298207 links:

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new If you want to explore the variant's impact on the transcript ENST00000753888.1, 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753888.1. 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

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000298207	ENST00000753888.1	n.150-24032C>T	intron	N/A
ENSG00000298207	ENST00000753889.1	n.150-24032C>T	intron	N/A
ENSG00000298207	ENST00000753890.1	n.246-24032C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0382

AC:

5806

AN:

152052

Hom.:

571

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00823

Gnomad AMI

AF:

0.0198

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.00979

Gnomad EAS

AF:

0.273

Gnomad SAS

AF:

0.0379

Gnomad FIN

AF:

0.00858

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0118

Gnomad OTH

AF:

0.0488

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

GnomAD4 genome

AF:

0.0382

AC:

5811

AN:

152170

Hom.:

577

Cov.:

AF XY:

0.0425

AC XY:

3164

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.00819

AC:

340

AN:

41534

American (AMR)

AF:

0.185

AC:

2825

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.00979

AC:

AN:

3472

East Asian (EAS)

AF:

0.273

AC:

1416

AN:

5178

South Asian (SAS)

AF:

0.0373

AC:

180

AN:

4822

European-Finnish (FIN)

AF:

0.00858

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0118

AC:

804

AN:

67990

Other (OTH)

AF:

0.0478

AC:

101

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

225

450

674

899

1124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<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:

0.00427

Hom.:

Bravo

AF:

0.0550

Asia WGS

AF:

0.138

AC:

479

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.73

(source)

DANN

Benign

0.39

PhyloP100

-0.69

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