dbSNP rs5899787: LOC105376214:n.721-77978dupA (chr9-108131271-C-CT) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The XR_001746881.2(LOC105376214):n.721-77978dupA variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.69 ( 36700 hom., cov: 0)

Consequence

LOC105376214
XR_001746881.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.67

Publications

3 publications found

Variant links:

Genes affected

LOC105376214 (HGNC:):

LOC105376214 links:

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new If you want to explore the variant's impact on the transcript XR_001746881.2, 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 = 0.934 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:

0.690

AC:

104840

AN:

151932

Hom.:

36642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.761

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.670

Gnomad ASJ

AF:

0.636

Gnomad EAS

AF:

0.957

Gnomad SAS

AF:

0.856

Gnomad FIN

AF:

0.659

Gnomad MID

AF:

0.658

Gnomad NFE

AF:

0.628

Gnomad OTH

AF:

0.682

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

GnomAD4 genome

AF:

0.690

AC:

104958

AN:

152050

Hom.:

36700

Cov.:

AF XY:

0.698

AC XY:

51897

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.762

AC:

31591

AN:

41474

American (AMR)

AF:

0.670

AC:

10232

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.636

AC:

2205

AN:

3466

East Asian (EAS)

AF:

0.957

AC:

4953

AN:

5178

South Asian (SAS)

AF:

0.856

AC:

4128

AN:

4822

European-Finnish (FIN)

AF:

0.659

AC:

6954

AN:

10558

Middle Eastern (MID)

AF:

0.667

AC:

196

AN:

294

European-Non Finnish (NFE)

AF:

0.628

AC:

42667

AN:

67966

Other (OTH)

AF:

0.684

AC:

1445

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1656

3311

4967

6622

8278

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

820

1640

2460

3280

4100

<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:

0.672

Hom.:

4220

Bravo

AF:

0.692

Asia WGS

AF:

0.899

AC:

3121

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.7

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