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GeneBe

rs10484554

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_926691.3(LOC112267902):n.964G>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 151,892 control chromosomes in the GnomAD database, including 1,330 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 0.12 ( 1330 hom., cov: 32)

Consequence

LOC112267902
XR_926691.3 splice_region, non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.95
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC112267902XR_926691.3 linkuse as main transcriptn.964G>A splice_region_variant, non_coding_transcript_exon_variant 3/5

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.124
AC:
18814
AN:
151774
Hom.:
1330
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.104
Gnomad AMI
AF:
0.221
Gnomad AMR
AF:
0.109
Gnomad ASJ
AF:
0.309
Gnomad EAS
AF:
0.0517
Gnomad SAS
AF:
0.165
Gnomad FIN
AF:
0.0999
Gnomad MID
AF:
0.239
Gnomad NFE
AF:
0.134
Gnomad OTH
AF:
0.136
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.124
AC:
18817
AN:
151892
Hom.:
1330
Cov.:
32
AF XY:
0.124
AC XY:
9221
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.104
Gnomad4 AMR
AF:
0.109
Gnomad4 ASJ
AF:
0.309
Gnomad4 EAS
AF:
0.0520
Gnomad4 SAS
AF:
0.164
Gnomad4 FIN
AF:
0.0999
Gnomad4 NFE
AF:
0.134
Gnomad4 OTH
AF:
0.134
Alfa
AF:
0.143
Hom.:
2975
Bravo
AF:
0.124
Asia WGS
AF:
0.0930
AC:
326
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
4.2
Dann
Benign
0.36

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: rs10484554; hg19: chr6-31274555; API