rs7298683

Variant names:

• chr12-97392077-G-C
• rs7298683
• ENST00000774538.1:n.77+5166G>C

Your query was ambiguous. Multiple possible variants found:

• chr12-97392077-G-C
• chr12-97392077-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000774538.1(RMST):​n.77+5166G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: RMST ENST00000774538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 0 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMST	ENST00000774538.1	n.77+5166G>C		intron_variant	Intron 1 of 3
RMST	ENST00000774539.1	n.77+5166G>C		intron_variant	Intron 1 of 1
RMST	ENST00000774540.1	n.200+5166G>C		intron_variant	Intron 2 of 2
RMST	ENST00000774541.1	n.230+5166G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.066
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7298683; hg19: chr12-97785855;