Genetic Variant LOC105371657:n.483-65709delA (chr1-189502601-TA-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The XR_002958413.2(LOC105371657):n.483-65709delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0024 in 107,786 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0024 ( 1 hom., cov: 31)

Consequence

LOC105371657
XR_002958413.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

0 publications found

Variant links:

COSMIC-nc: COSV66172302

Genes affected

LOC105371657 (HGNC:):

LOC105371657 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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:

0.00240

AC:

259

AN:

107782

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00346

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00158

Gnomad ASJ

AF:

0.00261

Gnomad EAS

AF:

0.00307

Gnomad SAS

AF:

0.00738

Gnomad FIN

AF:

0.00197

Gnomad MID

AF:

0.0152

Gnomad NFE

AF:

0.00167

Gnomad OTH

AF:

0.00336

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

GnomAD4 genome

AF:

0.00240

AC:

259

AN:

107786

Hom.:

Cov.:

AF XY:

0.00271

AC XY:

140

AN XY:

51716

show subpopulations

African (AFR)

AF:

0.00349

AC:

AN:

26338

American (AMR)

AF:

0.00158

AC:

AN:

10742

Ashkenazi Jewish (ASJ)

AF:

0.00261

AC:

AN:

2686

East Asian (EAS)

AF:

0.00309

AC:

AN:

3884

South Asian (SAS)

AF:

0.00741

AC:

AN:

3374

European-Finnish (FIN)

AF:

0.00197

AC:

AN:

6098

Middle Eastern (MID)

AF:

0.0106

AC:

AN:

188

European-Non Finnish (NFE)

AF:

0.00167

AC:

AN:

52214

Other (OTH)

AF:

0.00334

AC:

AN:

1496

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.413

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.0

Splicing

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

Publications

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1-189502601-TAAAAAAAAAAA-TAAAAAAAAAA

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