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GeneBe

rs1805007

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2_SupportingPM5PP3

The NM_002386.4(MC1R):c.451C>A(p.Arg151Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R151C) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)

Consequence

MC1R
NM_002386.4 missense

Scores

5
9
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.96

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 33.
PM5
?
Other missense variant is known to change same aminoacid residue: Variant chr16-89919709-C-T is described in Lovd as [Pathogenic].
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.776

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MC1RNM_002386.4 linkuse as main transcriptc.451C>A p.Arg151Ser missense_variant 1/1 ENST00000555147.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MC1RENST00000555147.2 linkuse as main transcriptc.451C>A p.Arg151Ser missense_variant 1/1 NM_002386.4 P1
MC1RENST00000555427.1 linkuse as main transcriptc.451C>A p.Arg151Ser missense_variant 3/45
MC1RENST00000639847.1 linkuse as main transcriptc.451C>A p.Arg151Ser missense_variant 3/35 P1

Frequencies

GnomAD3 genomes
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.47
BayesDel_addAF
Pathogenic
0.26
D
BayesDel_noAF
Uncertain
0.13
Cadd
Uncertain
24
Dann
Uncertain
1.0
Eigen
Uncertain
0.68
Eigen_PC
Uncertain
0.61
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.96
D;.;D;D
M_CAP
Benign
0.074
D
MetaRNN
Pathogenic
0.78
D;D;D;D
MetaSVM
Uncertain
-0.19
T
MutationTaster
Benign
1.0
D;D
PROVEAN
Pathogenic
-5.4
D;.;D;N
REVEL
Uncertain
0.47
Sift
Pathogenic
0.0
D;.;D;D
Sift4G
Pathogenic
0.0010
D;.;D;D
Polyphen
1.0
.;D;D;.
Vest4
0.73
MutPred
0.56
Loss of MoRF binding (P = 0.0694);Loss of MoRF binding (P = 0.0694);Loss of MoRF binding (P = 0.0694);Loss of MoRF binding (P = 0.0694);
MVP
0.82
MPC
0.11
ClinPred
1.0
D
GERP RS
4.8
Varity_R
0.94
gMVP
0.50

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: rs1805007; hg19: chr16-89986117; API