rs11109026

Positions:

• chr12-97439821-C-T

Variant summary

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

The ENST00000640149.1(RMST):​n.237+7887C>T 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 0.0195 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 ENST00000640149.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMST	ENST00000640149.1	n.237+7887C>T		intron_variant, non_coding_transcript_variant		5
RMST	ENST00000538559.6	n.282+7887C>T		intron_variant, non_coding_transcript_variant		5
RMST	ENST00000655366.1	n.298+7887C>T		intron_variant, non_coding_transcript_variant
RMST	ENST00000667306.1	n.51+7887C>T		intron_variant, non_coding_transcript_variant

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;