rs2117429

Variant summary

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

The NM_001131007.2(TMEM131L):​c.240-18273C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,046 control chromosomes in the GnomAD database, including 5,038 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 0.25 ( 5038 hom., cov: 32)

Consequence

TMEM131L
NM_001131007.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.536
Variant links:
Genes affected
TMEM131L (HGNC:29146): (transmembrane 131 like) Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of immature T cell proliferation in thymus. Located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TMEM131LNM_001131007.2 linkuse as main transcriptc.240-18273C>G intron_variant ENST00000409959.8
LOC105377498XR_939363.3 linkuse as main transcriptn.174-3707G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TMEM131LENST00000409959.8 linkuse as main transcriptc.240-18273C>G intron_variant 5 NM_001131007.2 A2A2VDJ0-5
TMEM131LENST00000409663.7 linkuse as main transcriptc.240-18273C>G intron_variant 5 P4A2VDJ0-1
TMEM131LENST00000445960.5 linkuse as main transcriptc.196-18273C>G intron_variant, NMD_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.254
AC:
38663
AN:
151928
Hom.:
5026
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.255
Gnomad AMI
AF:
0.249
Gnomad AMR
AF:
0.322
Gnomad ASJ
AF:
0.259
Gnomad EAS
AF:
0.313
Gnomad SAS
AF:
0.264
Gnomad FIN
AF:
0.252
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.234
Gnomad OTH
AF:
0.260
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.255
AC:
38713
AN:
152046
Hom.:
5038
Cov.:
32
AF XY:
0.254
AC XY:
18912
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.255
Gnomad4 AMR
AF:
0.323
Gnomad4 ASJ
AF:
0.259
Gnomad4 EAS
AF:
0.313
Gnomad4 SAS
AF:
0.263
Gnomad4 FIN
AF:
0.252
Gnomad4 NFE
AF:
0.234
Gnomad4 OTH
AF:
0.262
Alfa
AF:
0.229
Hom.:
512
Bravo
AF:
0.264
Asia WGS
AF:
0.296
AC:
1026
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.4
DANN
Benign
0.21

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs2117429; hg19: chr4-154452952; API