chr12-97486280-T-C

Variant names:

• chr12-97486280-T-C
• rs10777873
• ENST00000850890.1:n.268-6181T>C

Variant summary

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

The ENST00000850890.1(RMST):​n.268-6181T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,128 control chromosomes in the GnomAD database, including 52,792 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 0.83 (52792 hom., cov: 32)
• Consequence: RMST ENST00000850890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850890.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMST	NR_186063.1	MANE Select	n.268-6181T>C		intron	N/A
	RMST	NR_024037.3		n.442-6181T>C		intron	N/A
	RMST	NR_152618.2		n.208-6181T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMST	ENST00000850890.1	MANE Select	n.268-6181T>C		intron	N/A
	RMST	ENST00000548886.3	TSL:1	n.588-6181T>C		intron	N/A
	RMST	ENST00000538559.6	TSL:5	n.954-6181T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126143 AN: 152010 Hom.: 52731 Cov.: 32

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.830 AC: 126260 AN: 152128 Hom.: 52792 Cov.: 32 AF XY: 0.821 AC XY: 61033 AN XY: 74338

African (AFR) AF: 0.907 AC: 37658 AN: 41514

American (AMR) AF: 0.789 AC: 12054 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2968 AN: 3472

East Asian (EAS) AF: 0.587 AC: 3031 AN: 5166

South Asian (SAS) AF: 0.734 AC: 3537 AN: 4820

European-Finnish (FIN) AF: 0.751 AC: 7948 AN: 10580

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56170 AN: 67980

Other (OTH) AF: 0.848 AC: 1785 AN: 2106

Alfa AF: 0.822 Hom.: 37550

Bravo AF: 0.839

Asia WGS AF: 0.698 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10777873; hg19: chr12-97880058;