9-121565769-T-G

Variant summary

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

The XR_001746560.2(LOC107987016):​n.134+1082A>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 0.0559 in 152,104 control chromosomes in the GnomAD database, including 418 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 0.056 ( 418 hom., cov: 31)

Consequence

LOC107987016
XR_001746560.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310
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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107987016XR_001746560.2 linkuse as main transcriptn.134+1082A>C intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0558
AC:
8476
AN:
151986
Hom.:
413
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.130
Gnomad AMI
AF:
0.00549
Gnomad AMR
AF:
0.0281
Gnomad ASJ
AF:
0.0916
Gnomad EAS
AF:
0.0918
Gnomad SAS
AF:
0.0505
Gnomad FIN
AF:
0.0139
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0204
Gnomad OTH
AF:
0.0455
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0559
AC:
8506
AN:
152104
Hom.:
418
Cov.:
31
AF XY:
0.0557
AC XY:
4139
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.130
Gnomad4 AMR
AF:
0.0281
Gnomad4 ASJ
AF:
0.0916
Gnomad4 EAS
AF:
0.0917
Gnomad4 SAS
AF:
0.0495
Gnomad4 FIN
AF:
0.0139
Gnomad4 NFE
AF:
0.0204
Gnomad4 OTH
AF:
0.0450
Alfa
AF:
0.0462
Hom.:
28
Bravo
AF:
0.0603
Asia WGS
AF:
0.0660
AC:
232
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.91
DANN
Benign
0.33

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: rs7042542; hg19: chr9-124328048; API