12-97505598-T-G

Variant names:

• chr12-97505598-T-G
• rs10507089
• ENST00000548886.3:n.1153+10717T>G

Variant summary

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

The ENST00000548886.3(RMST):​n.1153+10717T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0749 in 152,332 control chromosomes in the GnomAD database, including 736 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 0.075 (736 hom., cov: 33)
• Consequence: RMST ENST00000548886.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RMST	NR_024037.3	n.1133+9542T>G		intron_variant	Intron 7 of 8
RMST	NR_152618.2	n.887+9542T>G		intron_variant	Intron 7 of 10
RMST	NR_186051.1	n.1086+9542T>G		intron_variant	Intron 10 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMST	ENST00000548886.3	n.1153+10717T>G		intron_variant	Intron 5 of 8	1
RMST	ENST00000538559.6	n.1523+10717T>G		intron_variant	Intron 9 of 13	5
RMST	ENST00000541282.5	n.803+9542T>G		intron_variant	Intron 7 of 8	2

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 11390 AN: 152214 Hom.: 731 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.0749 AC: 11407 AN: 152332 Hom.: 736 Cov.: 33 AF XY: 0.0751 AC XY: 5594 AN XY: 74506

African (AFR) AF: 0.153 AC: 6374 AN: 41568

American (AMR) AF: 0.0971 AC: 1486 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3472

East Asian (EAS) AF: 0.168 AC: 870 AN: 5188

South Asian (SAS) AF: 0.0964 AC: 466 AN: 4832

European-Finnish (FIN) AF: 0.0147 AC: 156 AN: 10624

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0251 AC: 1705 AN: 68028

Other (OTH) AF: 0.0763 AC: 161 AN: 2110

Alfa AF: 0.0331 Hom.: 58

Bravo AF: 0.0850

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.53
PhyloP100		-0.030
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10507089; hg19: chr12-97899376;