chr15-52952680-C-T

Variant summary

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

The XR_004837530.2(LOC107983981):​n.248-18723C>T 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 0.0511 in 152,282 control chromosomes in the GnomAD database, including 390 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 0.051 ( 390 hom., cov: 33)

Consequence

LOC107983981
XR_004837530.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.995
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107983981XR_004837530.2 linkuse as main transcriptn.248-18723C>T intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0511
AC:
7773
AN:
152164
Hom.:
390
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.110
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0773
Gnomad ASJ
AF:
0.0121
Gnomad EAS
AF:
0.185
Gnomad SAS
AF:
0.0164
Gnomad FIN
AF:
0.0137
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0101
Gnomad OTH
AF:
0.0502
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0511
AC:
7788
AN:
152282
Hom.:
390
Cov.:
33
AF XY:
0.0515
AC XY:
3832
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.110
Gnomad4 AMR
AF:
0.0779
Gnomad4 ASJ
AF:
0.0121
Gnomad4 EAS
AF:
0.185
Gnomad4 SAS
AF:
0.0162
Gnomad4 FIN
AF:
0.0137
Gnomad4 NFE
AF:
0.0101
Gnomad4 OTH
AF:
0.0516
Alfa
AF:
0.0385
Hom.:
34
Bravo
AF:
0.0626
Asia WGS
AF:
0.109
AC:
379
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.6
DANN
Benign
0.73

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: rs716188; hg19: chr15-53244877; API