12-97392077-G-T

Variant names:

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

Variant summary

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

The ENST00000774538.1(RMST):​n.77+5166G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 152,198 control chromosomes in the GnomAD database, including 70,851 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 0.96 (70851 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

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>T		intron_variant	Intron 1 of 3
RMST	ENST00000774539.1	n.77+5166G>T		intron_variant	Intron 1 of 1
RMST	ENST00000774540.1	n.200+5166G>T		intron_variant	Intron 2 of 2
RMST	ENST00000774541.1	n.230+5166G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146692 AN: 152080 Hom.: 70789 Cov.: 31

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.965 AC: 146813 AN: 152198 Hom.: 70851 Cov.: 31 AF XY: 0.963 AC XY: 71656 AN XY: 74386

African (AFR) AF: 0.991 AC: 41191 AN: 41558

American (AMR) AF: 0.973 AC: 14852 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3349 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5161 AN: 5166

South Asian (SAS) AF: 0.960 AC: 4622 AN: 4816

European-Finnish (FIN) AF: 0.916 AC: 9703 AN: 10598

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64684 AN: 68010

Other (OTH) AF: 0.976 AC: 2061 AN: 2112

Alfa AF: 0.959 Hom.: 114788

Bravo AF: 0.972

Asia WGS AF: 0.983 AC: 3420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.28
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;