X-48638775-C-T

Variant summary

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

The XR_001755842.2(LOC107985695):​n.3093C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 110,319 control chromosomes in the GnomAD database, including 7,299 homozygotes. There are 12,894 hemizygotes in GnomAD. 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 0.41 ( 7299 hom., 12894 hem., cov: 22)

Consequence

LOC107985695
XR_001755842.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.668
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC107985695XR_001755842.2 linkuse as main transcriptn.3093C>T non_coding_transcript_exon_variant 3/3
LOC107985695XR_007068227.1 linkuse as main transcriptn.3089C>T non_coding_transcript_exon_variant 3/3
use as main transcriptn.48638775C>T intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.411
AC:
45291
AN:
110263
Hom.:
7292
Cov.:
22
AF XY:
0.395
AC XY:
12852
AN XY:
32535
show subpopulations
Gnomad AFR
AF:
0.573
Gnomad AMI
AF:
0.278
Gnomad AMR
AF:
0.375
Gnomad ASJ
AF:
0.213
Gnomad EAS
AF:
0.437
Gnomad SAS
AF:
0.338
Gnomad FIN
AF:
0.337
Gnomad MID
AF:
0.196
Gnomad NFE
AF:
0.348
Gnomad OTH
AF:
0.368
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.411
AC:
45344
AN:
110319
Hom.:
7299
Cov.:
22
AF XY:
0.396
AC XY:
12894
AN XY:
32599
show subpopulations
Gnomad4 AFR
AF:
0.574
Gnomad4 AMR
AF:
0.376
Gnomad4 ASJ
AF:
0.213
Gnomad4 EAS
AF:
0.437
Gnomad4 SAS
AF:
0.337
Gnomad4 FIN
AF:
0.337
Gnomad4 NFE
AF:
0.348
Gnomad4 OTH
AF:
0.366
Alfa
AF:
0.270
Hom.:
1743
Bravo
AF:
0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.5
DANN
Benign
0.80

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: rs1395950; hg19: chrX-48497163; API