Variant 15-31049313-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001252024.2(TRPM1):c.1572+62G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 1,610,592 control chromosomes in the GnomAD database, including 242,158 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.47 ( 18747 hom., cov: 32)

Exomes 𝑓: 0.55 ( 223411 hom. )

Consequence

TRPM1
NM_001252024.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.252

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]

TRPM1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 15-31049313-C-T is Benign according to our data. Variant chr15-31049313-C-T is described in ClinVar as [Benign]. Clinvar id is 1261772.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
TRPM1	NM_001252024.2 linkuse as main transcript	c.1572+62G>A	intron_variant	ENST00000256552.11
TRPM1	NM_001252020.2 linkuse as main transcript	c.1623+62G>A	intron_variant
TRPM1	NM_002420.6 linkuse as main transcript	c.1506+62G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM1	ENST00000256552.11 linkuse as main transcript	c.1572+62G>A		intron_variant		1	NM_001252024.2	P4	Q7Z4N2-6

Frequencies

GnomAD3 genomes

AF:

0.466

AC:

70884

AN:

151968

Hom.:

18751

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.406

Gnomad AMR

AF:

0.565

Gnomad ASJ

AF:

0.554

Gnomad EAS

AF:

0.940

Gnomad SAS

AF:

0.505

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.547

Gnomad OTH

AF:

0.497

GnomAD4 exome

AF:

0.546

AC:

797028

AN:

1458504

Hom.:

223411

AF XY:

0.545

AC XY:

395415

AN XY:

725712

show subpopulations

Gnomad4 AFR exome

AF:

0.187

Gnomad4 AMR exome

AF:

0.589

Gnomad4 ASJ exome

AF:

0.551

Gnomad4 EAS exome

AF:

0.909

Gnomad4 SAS exome

AF:

0.476

Gnomad4 FIN exome

AF:

0.536

Gnomad4 NFE exome

AF:

0.549

Gnomad4 OTH exome

AF:

0.545

GnomAD4 genome

AF:

0.466

AC:

70901

AN:

152088

Hom.:

18747

Cov.:

AF XY:

0.470

AC XY:

34957

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.207

Gnomad4 AMR

AF:

0.565

Gnomad4 ASJ

AF:

0.554

Gnomad4 EAS

AF:

0.940

Gnomad4 SAS

AF:

0.505

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.547

Gnomad4 OTH

AF:

0.497

Alfa

AF:

0.460

Hom.:

2576

Bravo

AF:

0.458

Asia WGS

AF:

0.649

AC:

2252

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.34

DANN

Benign

0.53

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over