15-31030659-T-C

Variant summary

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

The NM_001252024.2(TRPM1):​c.3127+324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,008 control chromosomes in the GnomAD database, including 15,008 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 0.40 ( 15008 hom., cov: 32)

Consequence

TRPM1
NM_001252024.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.657
Variant links:
Genes affected
TRPM1 (HGNC:7146): (transient receptor potential cation channel subfamily M member 1) This gene encodes a member of the transient receptor potential melastatin subfamily of transient receptor potential ion channels. The encoded protein is a calcium permeable cation channel that is expressed in melanocytes and may play a role in melanin synthesis. Specific mutations in this gene are the cause autosomal recessive complete congenital stationary night blindness-1C. The expression of this protein is inversely correlated with melanoma aggressiveness and as such it is used as a prognostic marker for melanoma metastasis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]

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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRPM1NM_001252024.2 linkc.3127+324A>G intron_variant ENST00000256552.11 NP_001238953.1 Q7Z4N2-6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRPM1ENST00000256552.11 linkc.3127+324A>G intron_variant 1 NM_001252024.2 ENSP00000256552.7 Q7Z4N2-6

Frequencies

GnomAD3 genomes
AF:
0.396
AC:
60189
AN:
151890
Hom.:
14960
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.709
Gnomad AMI
AF:
0.209
Gnomad AMR
AF:
0.325
Gnomad ASJ
AF:
0.331
Gnomad EAS
AF:
0.144
Gnomad SAS
AF:
0.332
Gnomad FIN
AF:
0.151
Gnomad MID
AF:
0.364
Gnomad NFE
AF:
0.290
Gnomad OTH
AF:
0.386
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.397
AC:
60297
AN:
152008
Hom.:
15008
Cov.:
32
AF XY:
0.385
AC XY:
28591
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.709
Gnomad4 AMR
AF:
0.325
Gnomad4 ASJ
AF:
0.331
Gnomad4 EAS
AF:
0.144
Gnomad4 SAS
AF:
0.332
Gnomad4 FIN
AF:
0.151
Gnomad4 NFE
AF:
0.290
Gnomad4 OTH
AF:
0.384
Alfa
AF:
0.337
Hom.:
2803
Bravo
AF:
0.419
Asia WGS
AF:
0.309
AC:
1073
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.2
DANN
Benign
0.80

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: rs2042613; hg19: chr15-31322862; API