rs12143114

Variant summary

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

The NR_037845.1(LOC100506023):​n.656-45346A>G 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 0.307 in 152,022 control chromosomes in the GnomAD database, including 7,695 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 0.31 ( 7695 hom., cov: 32)

Consequence

LOC100506023
NR_037845.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.205
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=-0.8).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC100506023NR_037845.1 linkuse as main transcriptn.656-45346A>G intron_variant, non_coding_transcript_variant
TNFSF4XM_047429896.1 linkuse as main transcriptc.148-78184A>G intron_variant
TNFSF4XM_047429902.1 linkuse as main transcriptc.19-78184A>G intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.307
AC:
46616
AN:
151904
Hom.:
7687
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.190
Gnomad AMI
AF:
0.363
Gnomad AMR
AF:
0.399
Gnomad ASJ
AF:
0.284
Gnomad EAS
AF:
0.268
Gnomad SAS
AF:
0.310
Gnomad FIN
AF:
0.370
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.350
Gnomad OTH
AF:
0.312
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.307
AC:
46651
AN:
152022
Hom.:
7695
Cov.:
32
AF XY:
0.310
AC XY:
23007
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.190
Gnomad4 AMR
AF:
0.400
Gnomad4 ASJ
AF:
0.284
Gnomad4 EAS
AF:
0.267
Gnomad4 SAS
AF:
0.311
Gnomad4 FIN
AF:
0.370
Gnomad4 NFE
AF:
0.350
Gnomad4 OTH
AF:
0.315
Alfa
AF:
0.331
Hom.:
1763
Bravo
AF:
0.307
Asia WGS
AF:
0.289
AC:
1004
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
9.2
DANN
Benign
0.76

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: rs12143114; hg19: chr1-173254508; API