chr12-97444907-A-C

Variant names:

• chr12-97444907-A-C
• rs10777864
• ENST00000538559.6:n.282+12973A>C

Variant summary

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

The ENST00000655366.1(RMST):​n.298+12973A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,004 control chromosomes in the GnomAD database, including 18,037 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 0.48 (18037 hom., cov: 32)
• Consequence: RMST ENST00000655366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655366.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMST	ENST00000538559.6	TSL:5	n.282+12973A>C		intron	N/A
	RMST	ENST00000640149.1	TSL:5	n.237+12973A>C		intron	N/A
	RMST	ENST00000655366.1		n.298+12973A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72549 AN: 151886 Hom.: 17997 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.478 AC: 72642 AN: 152004 Hom.: 18037 Cov.: 32 AF XY: 0.480 AC XY: 35693 AN XY: 74302

African (AFR) AF: 0.601 AC: 24921 AN: 41438

American (AMR) AF: 0.492 AC: 7522 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2916 AN: 5154

South Asian (SAS) AF: 0.585 AC: 2823 AN: 4828

European-Finnish (FIN) AF: 0.331 AC: 3500 AN: 10576

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27776 AN: 67946

Other (OTH) AF: 0.485 AC: 1027 AN: 2116

Alfa AF: 0.435 Hom.: 32282

Bravo AF: 0.497

Asia WGS AF: 0.584 AC: 2026 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.32
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs10777864; hg19: chr12-97838685;