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GeneBe

rs25531

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The XR_001752824.2(LOC105371720):n.280+258T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.19 ( 468 hom., cov: 4)

Consequence

LOC105371720
XR_001752824.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.732
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 17-30237328-T-C is Benign according to our data. Variant chr17-30237328-T-C is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105371720XR_001752824.2 linkuse as main transcriptn.280+258T>C intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.187
AC:
5881
AN:
31434
Hom.:
464
Cov.:
4
show subpopulations
Gnomad AFR
AF:
0.292
Gnomad AMI
AF:
0.115
Gnomad AMR
AF:
0.179
Gnomad ASJ
AF:
0.0853
Gnomad EAS
AF:
0.318
Gnomad SAS
AF:
0.292
Gnomad FIN
AF:
0.192
Gnomad MID
AF:
0.0938
Gnomad NFE
AF:
0.129
Gnomad OTH
AF:
0.187
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.187
AC:
5896
AN:
31456
Hom.:
468
Cov.:
4
AF XY:
0.196
AC XY:
2750
AN XY:
13996
show subpopulations
Gnomad4 AFR
AF:
0.293
Gnomad4 AMR
AF:
0.179
Gnomad4 ASJ
AF:
0.0853
Gnomad4 EAS
AF:
0.321
Gnomad4 SAS
AF:
0.292
Gnomad4 FIN
AF:
0.192
Gnomad4 NFE
AF:
0.129
Gnomad4 OTH
AF:
0.186
Alfa
AF:
0.0264
Hom.:
20
Bravo
AF:
0.119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
Cadd
Benign
5.5
Dann
Benign
0.41

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: rs25531; hg19: chr17-28564346; API