rs10507088

Variant names:

• chr12-97485966-G-A
• rs10507088
• ENST00000548886.3:n.588-6495G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000548886.3(RMST):​n.588-6495G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,156 control chromosomes in the GnomAD database, including 6,080 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 0.26 (6080 hom., cov: 33)
• Consequence: RMST ENST00000548886.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 1 publications found

Genes affected

RMST (HGNC:29893): (rhabdomyosarcoma 2 associated transcript) This gene produces a long non-coding RNA that functions in neurogenesis by aiding in the association of Sox2 transcription factor to its target promoters. [provided by RefSeq, Dec 2017]

ENSG00000300902 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RMST	NR_024037.3	n.442-6495G>A		intron_variant	Intron 2 of 8
RMST	NR_152618.2	n.208-6495G>A		intron_variant	Intron 2 of 10
RMST	NR_186051.1	n.325+2478G>A		intron_variant	Intron 4 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMST	ENST00000548886.3	n.588-6495G>A		intron_variant	Intron 1 of 8	1
RMST	ENST00000538559.6	n.954-6495G>A		intron_variant	Intron 5 of 13	5
RMST	ENST00000541282.5	n.112-6495G>A		intron_variant	Intron 2 of 8	2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40051 AN: 152038 Hom.: 6074 Cov.: 33

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.263 AC: 40093 AN: 152156 Hom.: 6080 Cov.: 33 AF XY: 0.264 AC XY: 19611 AN XY: 74388

African (AFR) AF: 0.415 AC: 17217 AN: 41502

American (AMR) AF: 0.220 AC: 3366 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5174

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2145 AN: 10586

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13375 AN: 68002

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.214 Hom.: 2389

Bravo AF: 0.271

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs10507088; hg19: chr12-97879744;