rs12750070

Variant summary

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

The NR_037845.1(LOC100506023):​n.656-40610G>A 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 0.298 in 151,924 control chromosomes in the GnomAD database, including 7,323 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 0.30 ( 7323 hom., cov: 32)

Consequence

LOC100506023
NR_037845.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368
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=-0.96).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC100506023NR_037845.1 linkuse as main transcriptn.656-40610G>A intron_variant, non_coding_transcript_variant
TNFSF4XM_047429896.1 linkuse as main transcriptc.148-73448G>A intron_variant
TNFSF4XM_047429902.1 linkuse as main transcriptc.19-73448G>A intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.298
AC:
45208
AN:
151806
Hom.:
7317
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.365
Gnomad AMR
AF:
0.396
Gnomad ASJ
AF:
0.279
Gnomad EAS
AF:
0.268
Gnomad SAS
AF:
0.310
Gnomad FIN
AF:
0.349
Gnomad MID
AF:
0.274
Gnomad NFE
AF:
0.346
Gnomad OTH
AF:
0.308
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.298
AC:
45241
AN:
151924
Hom.:
7323
Cov.:
32
AF XY:
0.300
AC XY:
22273
AN XY:
74220
show subpopulations
Gnomad4 AFR
AF:
0.172
Gnomad4 AMR
AF:
0.397
Gnomad4 ASJ
AF:
0.279
Gnomad4 EAS
AF:
0.267
Gnomad4 SAS
AF:
0.310
Gnomad4 FIN
AF:
0.349
Gnomad4 NFE
AF:
0.346
Gnomad4 OTH
AF:
0.310
Alfa
AF:
0.328
Hom.:
2878
Bravo
AF:
0.300
Asia WGS
AF:
0.287
AC:
998
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.26
DANN
Benign
0.71

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: rs12750070; hg19: chr1-173249772; API