Genetic Variant ENST00000558445.6:c.16C>T (chr15-31160944-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000558445.6(TRPM1):c.16C>T(p.Arg6Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,534,778 control chromosomes in the GnomAD database, including 15,007 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1047 hom., cov: 33)

Exomes 𝑓: 0.14 ( 13960 hom. )

Consequence

TRPM1
ENST00000558445.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.33

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003954917).

BP6

Variant 15-31160944-G-A is Benign according to our data. Variant chr15-31160944-G-A is described in ClinVar as [Benign]. Clinvar id is 1297788.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPM1	NM_001252020.2 link	c.16C>T	p.Arg6Trp	missense_variant	Exon 1 of 27		NP_001238949.1	Q7Z4N2-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPM1	ENST00000558445.6 link	c.16C>T	p.Arg6Trp	missense_variant	Exon 1 of 27	1		ENSP00000452946.2		Q7Z4N2-5H0YKU7
TRPM1	ENST00000559177.6 link	c.16C>T	p.Arg6Trp	missense_variant	Exon 1 of 8	5		ENSP00000453477.2		H0YM61

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15999

AN:

152152

Hom.:

1049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0465

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.0963

Gnomad EAS

AF:

0.0154

Gnomad SAS

AF:

0.0581

Gnomad FIN

AF:

0.162

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.126

GnomAD3 exomes

AF:

0.102

AC:

13117

AN:

128012

Hom.:

795

AF XY:

0.103

AC XY:

7251

AN XY:

70094

show subpopulations

Gnomad AFR exome

AF:

0.0414

Gnomad AMR exome

AF:

0.0859

Gnomad ASJ exome

AF:

0.0985

Gnomad EAS exome

AF:

0.0181

Gnomad SAS exome

AF:

0.0747

Gnomad FIN exome

AF:

0.164

Gnomad NFE exome

AF:

0.142

Gnomad OTH exome

AF:

0.124

GnomAD4 exome

AF:

0.136

AC:

187827

AN:

1382506

Hom.:

13960

Cov.:

AF XY:

0.134

AC XY:

91470

AN XY:

682198

show subpopulations

Gnomad4 AFR exome

AF:

0.0431

Gnomad4 AMR exome

AF:

0.0892

Gnomad4 ASJ exome

AF:

0.0945

Gnomad4 EAS exome

AF:

0.0125

Gnomad4 SAS exome

AF:

0.0729

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.149

Gnomad4 OTH exome

AF:

0.127

GnomAD4 genome

AF:

0.105

AC:

15990

AN:

152272

Hom.:

1047

Cov.:

AF XY:

0.105

AC XY:

7804

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0463

Gnomad4 AMR

AF:

0.109

Gnomad4 ASJ

AF:

0.0963

Gnomad4 EAS

AF:

0.0155

Gnomad4 SAS

AF:

0.0580

Gnomad4 FIN

AF:

0.162

Gnomad4 NFE

AF:

0.141

Gnomad4 OTH

AF:

0.124

Alfa

AF:

0.124

Hom.:

265

Bravo

AF:

0.0999

TwinsUK

AF:

0.152

AC:

564

ALSPAC

AF:

0.148

AC:

569

ExAC

AF:

0.0672

AC:

1104

Asia WGS

AF:

0.0440

AC:

152

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Uncertain

1.0

Eigen

Benign

-0.33

Eigen_PC

Benign

-0.38

FATHMM_MKL

Benign

0.63

LIST_S2

Benign

0.70

MetaRNN

Benign

0.0040

MetaSVM

Benign

-1.0

PrimateAI

Uncertain

0.58

PROVEAN

Benign

-0.84

REVEL

Benign

0.067

Sift

Uncertain

0.0030

Sift4G

Uncertain

0.0090

Vest4

0.14

MPC

0.75

ClinPred

0.045

GERP RS

-0.92

gMVP

0.33

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.

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