chr9-15157979-T-C

Variant summary

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

The XR_007061423.1(LOC124902123):​n.236-4928T>C 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 0.0779 in 151,056 control chromosomes in the GnomAD database, including 706 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 0.078 ( 706 hom., cov: 32)

Consequence

LOC124902123
XR_007061423.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.267
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=-0.75).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0843 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124902123XR_007061423.1 linkuse as main transcriptn.236-4928T>C intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0779
AC:
11751
AN:
150938
Hom.:
704
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0818
Gnomad AMI
AF:
0.198
Gnomad AMR
AF:
0.0483
Gnomad ASJ
AF:
0.0346
Gnomad EAS
AF:
0.0779
Gnomad SAS
AF:
0.0505
Gnomad FIN
AF:
0.0724
Gnomad MID
AF:
0.0637
Gnomad NFE
AF:
0.0861
Gnomad OTH
AF:
0.0618
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0779
AC:
11762
AN:
151056
Hom.:
706
Cov.:
32
AF XY:
0.0759
AC XY:
5607
AN XY:
73852
show subpopulations
Gnomad4 AFR
AF:
0.0818
Gnomad4 AMR
AF:
0.0482
Gnomad4 ASJ
AF:
0.0346
Gnomad4 EAS
AF:
0.0781
Gnomad4 SAS
AF:
0.0505
Gnomad4 FIN
AF:
0.0724
Gnomad4 NFE
AF:
0.0861
Gnomad4 OTH
AF:
0.0611
Alfa
AF:
0.0778
Hom.:
680
Bravo
AF:
0.0766
Asia WGS
AF:
0.0540
AC:
186
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
5.4
DANN
Benign
0.94

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: rs1780159; hg19: chr9-15157977; API