12-97486280-T-C

Position:

• chr12-97486280-T-C

Variant summary

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

The NR_152618.1(RMST):​n.236-6181T>C 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 0.83 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 NR_152618.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RMST	NR_152618.1	n.236-6181T>C		intron_variant, non_coding_transcript_variant
RMST	NR_024037.2	n.113-6181T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMST	ENST00000640149.1	n.645-6181T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.848

Alfa AF: 0.823 Hom.: 26287

Bravo AF: 0.839

Asia WGS AF: 0.698 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10777873; hg19: chr12-97880058;