rs3212359

chr16-89918769-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XM_047435031.1(LOC124903759):c.1213-82C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 234,560 control chromosomes in the GnomAD database, including 25,068 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.45 (16512 hom., cov: 34)
  • Exomes 𝑓: 0.42 (8556 hom.)
• Consequence: LOC124903759 XM_047435031.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.48

Genes affected

LOC124903759 (HGNC:):

MC1R (HGNC:6929): (melanocortin 1 receptor) This intronless gene encodes the receptor protein for melanocyte-stimulating hormone (MSH). The encoded protein, a seven pass transmembrane G protein coupled receptor, controls melanogenesis. Two types of melanin exist: red pheomelanin and black eumelanin. Gene mutations that lead to a loss in function are associated with increased pheomelanin production, which leads to lighter skin and hair color. Eumelanin is photoprotective but pheomelanin may contribute to UV-induced skin damage by generating free radicals upon UV radiation. Binding of MSH to its receptor activates the receptor and stimulates eumelanin synthesis. This receptor is a major determining factor in sun sensitivity and is a genetic risk factor for melanoma and non-melanoma skin cancer. Over 30 variant alleles have been identified which correlate with skin and hair color, providing evidence that this gene is an important component in determining normal human pigment variation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 16-89918769-C-T is Benign according to our data. Variant chr16-89918769-C-T is described in ClinVar as [Benign]. Clinvar id is 321402.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903759	XM_047435031.1	c.1213-82C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MC1R	ENST00000555427.1	c.-408-82C>T		intron_variant		5
MC1R	ENST00000639847.1	c.-408-82C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68232 AN: 152036 Hom.: 16484 Cov.: 34

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.430

GnomAD4 exome AF: 0.421 AC: 34680 AN: 82406 Hom.: 8556 Cov.: 0 AF XY: 0.419 AC XY: 15924 AN XY: 37982

Gnomad4 AFR exome AF: 0.593

Gnomad4 AMR exome AF: 0.549

Gnomad4 ASJ exome AF: 0.341

Gnomad4 EAS exome AF: 0.795

Gnomad4 SAS exome AF: 0.529

Gnomad4 FIN exome AF: 0.463

Gnomad4 NFE exome AF: 0.328

Gnomad4 OTH exome AF: 0.382

GnomAD4 genome AF: 0.449 AC: 68310 AN: 152154 Hom.: 16512 Cov.: 34 AF XY: 0.457 AC XY: 34009 AN XY: 74390

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.431

Alfa AF: 0.414 Hom.: 2000

Bravo AF: 0.460

Asia WGS AF: 0.564 AC: 1965 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Melanoma, cutaneous malignant, susceptibility to, 5 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	0.43
Dann	Benign	0.86

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

Other links and lift over

dbSNP: rs3212359; hg19: chr16-89985177; COSMIC: COSV59624817; COSMIC: COSV59624817;