dbSNP rs4016810: LOC107984219:n.5354-10717_5354-10716delGT (chr10-32007305-CTG-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The XR_001747415.2(LOC107984219):n.5354-10717_5354-10716delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 17242 hom., cov: 0)

Consequence

LOC107984219
XR_001747415.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0580

Publications

0 publications found

Variant links:

Genes affected

LOC107984219 (HGNC:):

LOC107984219 links:

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new If you want to explore the variant's impact on the transcript XR_001747415.2, 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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes

AF:

0.470

AC:

71056

AN:

151290

Hom.:

17242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.350

Gnomad AMI

AF:

0.540

Gnomad AMR

AF:

0.478

Gnomad ASJ

AF:

0.472

Gnomad EAS

AF:

0.605

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.595

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.470

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

GnomAD4 genome

AF:

0.469

AC:

71079

AN:

151408

Hom.:

17242

Cov.:

AF XY:

0.474

AC XY:

35046

AN XY:

73930

show subpopulations

African (AFR)

AF:

0.350

AC:

14445

AN:

41264

American (AMR)

AF:

0.477

AC:

7267

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.472

AC:

1636

AN:

3464

East Asian (EAS)

AF:

0.605

AC:

3105

AN:

5130

South Asian (SAS)

AF:

0.495

AC:

2374

AN:

4798

European-Finnish (FIN)

AF:

0.595

AC:

6196

AN:

10416

Middle Eastern (MID)

AF:

0.466

AC:

137

AN:

294

European-Non Finnish (NFE)

AF:

0.508

AC:

34447

AN:

67812

Other (OTH)

AF:

0.468

AC:

984

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1826

3652

5478

7304

9130

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<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:

0.492

Hom.:

2269

Bravo

AF:

0.456

Asia WGS

AF:

0.516

AC:

1790

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.058

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