GeneBe

rs10548381

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_007063255.1(LOC124902906):​n.176+942_176+944del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,252 control chromosomes in the GnomAD database, including 517 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.078 ( 517 hom., cov: 30)

Consequence

LOC124902906
XR_007063255.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.519
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC124902906XR_007063255.1 linkuse as main transcriptn.176+942_176+944del intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0781
AC:
11876
AN:
152134
Hom.:
517
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0426
Gnomad AMI
AF:
0.156
Gnomad AMR
AF:
0.0535
Gnomad ASJ
AF:
0.0766
Gnomad EAS
AF:
0.0406
Gnomad SAS
AF:
0.0491
Gnomad FIN
AF:
0.105
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.105
Gnomad OTH
AF:
0.0651
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0780
AC:
11876
AN:
152252
Hom.:
517
Cov.:
30
AF XY:
0.0773
AC XY:
5754
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.0425
Gnomad4 AMR
AF:
0.0534
Gnomad4 ASJ
AF:
0.0766
Gnomad4 EAS
AF:
0.0407
Gnomad4 SAS
AF:
0.0491
Gnomad4 FIN
AF:
0.105
Gnomad4 NFE
AF:
0.105
Gnomad4 OTH
AF:
0.0649
Alfa
AF:
0.103
Hom.:
110
Bravo
AF:
0.0710
Asia WGS
AF:
0.0450
AC:
156
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10548381; hg19: chr12-27484610; API