rs11109072

Positions:

• chr12-97507492-C-A
• chr12-97507492-C-T

Variant summary

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

The ENST00000548886.2(RMST):​n.573+12611C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 151,762 control chromosomes in the GnomAD database, including 1,762 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 0.12 (1762 hom., cov: 31)
• Consequence: RMST ENST00000548886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RMST	NR_024037.3	n.1133+11436C>A		intron_variant
RMST	NR_152618.2	n.887+11436C>A		intron_variant
RMST	NR_186051.1	n.1086+11436C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMST	ENST00000548886.2	n.573+12611C>A		intron_variant		1
RMST	ENST00000538559.6	n.1523+12611C>A		intron_variant		5
RMST	ENST00000541282.5	n.803+11436C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17575 AN: 151644 Hom.: 1756 Cov.: 31

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0622

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.116 AC: 17598 AN: 151762 Hom.: 1762 Cov.: 31 AF XY: 0.117 AC XY: 8686 AN XY: 74156

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0622

Gnomad4 NFE AF: 0.0357

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0934 Hom.: 158

Bravo AF: 0.128

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.15
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11109072; hg19: chr12-97901270;