rs13358880

chr5-57513472-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506106.1(RMEL3):n.408+16555G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,110 control chromosomes in the GnomAD database, including 1,094 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 0.11 (1094 hom., cov: 32)
• Consequence: RMEL3 ENST00000506106.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

RMEL3 (HGNC:53975): (enriched in melanoma 3)

LOC102724122 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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/exons	MANE	UniProt
LOC102724122	XR_007059132.1	n.1211+711G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMEL3	ENST00000506106.1	n.408+16555G>A		intron_variant, non_coding_transcript_variant		2
RMEL3	ENST00000664944.1	n.599+16555G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16602 AN: 151990 Hom.: 1093 Cov.: 32

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.115

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.109 AC: 16623 AN: 152110 Hom.: 1094 Cov.: 32 AF XY: 0.110 AC XY: 8185 AN XY: 74358

Gnomad4 AFR AF: 0.0504

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.00329

Gnomad4 SAS AF: 0.0776

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.114

Alfa AF: 0.124 Hom.: 211

Bravo AF: 0.104

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	4.7
Dann	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13358880; hg19: chr5-56809299;