chr12-97507492-C-A

Variant names:

• chr12-97507492-C-A
• rs11109072
• ENST00000548886.3:n.1153+12611C>A

Variant summary

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

The ENST00000548886.3(RMST):​n.1153+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 ENST00000548886.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 18 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=-0.88).
• 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 rank	MANE	Protein	UniProt
RMST	NR_024037.3	n.1133+11436C>A		intron_variant	Intron 7 of 8
RMST	NR_152618.2	n.887+11436C>A		intron_variant	Intron 7 of 10
RMST	NR_186051.1	n.1086+11436C>A		intron_variant	Intron 10 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMST	ENST00000548886.3	n.1153+12611C>A		intron_variant	Intron 5 of 8	1
RMST	ENST00000538559.6	n.1523+12611C>A		intron_variant	Intron 9 of 13	5
RMST	ENST00000541282.5	n.803+11436C>A		intron_variant	Intron 7 of 8	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

African (AFR) AF: 0.253 AC: 10456 AN: 41322

American (AMR) AF: 0.115 AC: 1747 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3464

East Asian (EAS) AF: 0.249 AC: 1281 AN: 5150

South Asian (SAS) AF: 0.106 AC: 510 AN: 4802

European-Finnish (FIN) AF: 0.0622 AC: 655 AN: 10534

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0357 AC: 2429 AN: 67948

Other (OTH) AF: 0.113 AC: 239 AN: 2110

Alfa AF: 0.0762 Hom.: 1547

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11109072; hg19: chr12-97901270;