rs11109026

Variant names:

• chr12-97439821-C-T
• rs11109026
• ENST00000538559.6:n.282+7887C>T

Variant summary

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

The ENST00000538559.6(RMST):​n.282+7887C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0195 in 151,486 control chromosomes in the GnomAD database, including 110 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 0.019 (110 hom., cov: 32)
• Consequence: RMST ENST00000538559.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.973

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0666 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	ENST00000538559.6	n.282+7887C>T		intron_variant	Intron 1 of 13	5
RMST	ENST00000640149.1	n.237+7887C>T		intron_variant	Intron 2 of 13	5
RMST	ENST00000655366.1	n.298+7887C>T		intron_variant	Intron 1 of 3
RMST	ENST00000667306.1	n.51+7887C>T		intron_variant	Intron 1 of 13

Frequencies

GnomAD3 genomes AF: 0.0195 AC: 2945 AN: 151368 Hom.: 110 Cov.: 32

Gnomad AFR AF: 0.0687

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00494

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.0125

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

GnomAD4 genome AF: 0.0195 AC: 2953 AN: 151486 Hom.: 110 Cov.: 32 AF XY: 0.0187 AC XY: 1381 AN XY: 74046

Gnomad4 AFR AF: 0.0687

Gnomad4 AMR AF: 0.00493

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000416

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000206

Gnomad4 OTH AF: 0.0124

Alfa AF: 0.0155 Hom.: 4

Bravo AF: 0.0225

Asia WGS AF: 0.00380 AC: 13 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11109026; hg19: chr12-97833599;