rs9288534

Variant summary

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

The XR_007088689.1(LOC105373703):​n.635-26626C>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 0.364 in 151,874 control chromosomes in the GnomAD database, including 11,085 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 0.36 ( 11085 hom., cov: 32)

Consequence

LOC105373703
XR_007088689.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105373703XR_007088689.1 linkuse as main transcriptn.635-26626C>T intron_variant, non_coding_transcript_variant
LOC105373703XR_001739749.2 linkuse as main transcriptn.852C>T non_coding_transcript_exon_variant 5/8
LOC105373703XR_001739750.2 linkuse as main transcriptn.852C>T non_coding_transcript_exon_variant 5/6
LOC105373703XR_001739751.2 linkuse as main transcriptn.852C>T non_coding_transcript_exon_variant 5/7

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.364
AC:
55170
AN:
151756
Hom.:
11058
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.510
Gnomad AMI
AF:
0.189
Gnomad AMR
AF:
0.331
Gnomad ASJ
AF:
0.304
Gnomad EAS
AF:
0.568
Gnomad SAS
AF:
0.478
Gnomad FIN
AF:
0.332
Gnomad MID
AF:
0.316
Gnomad NFE
AF:
0.269
Gnomad OTH
AF:
0.356
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.364
AC:
55246
AN:
151874
Hom.:
11085
Cov.:
32
AF XY:
0.371
AC XY:
27547
AN XY:
74226
show subpopulations
Gnomad4 AFR
AF:
0.510
Gnomad4 AMR
AF:
0.331
Gnomad4 ASJ
AF:
0.304
Gnomad4 EAS
AF:
0.568
Gnomad4 SAS
AF:
0.478
Gnomad4 FIN
AF:
0.332
Gnomad4 NFE
AF:
0.269
Gnomad4 OTH
AF:
0.360
Alfa
AF:
0.285
Hom.:
6559
Bravo
AF:
0.367
Asia WGS
AF:
0.492
AC:
1713
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.1
DANN
Benign
0.29

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: rs9288534; hg19: chr2-156697282; API