2-207234773-C-T

Variant names:

• chr2-207234773-C-T
• rs991684
• ENST00000448786.1:n.467+665G>A

Variant summary

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

The ENST00000448786.1(MYOSLID-AS1):​n.467+665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,036 control chromosomes in the GnomAD database, including 6,832 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 0.30 (6832 hom., cov: 32)
• Consequence: MYOSLID-AS1 ENST00000448786.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 8 publications found

Genes affected

MYOSLID-AS1 (HGNC:):

MYOSLID (HGNC:51821): (myocardin-induced smooth muscle lncRNA, inducer of differentiation)

MYOSLID-AS1 (HGNC:54063): (MYOSLID antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448786.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYOSLID-AS1	NR_110283.1		n.302+3047G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYOSLID-AS1	ENST00000448786.1	TSL:1	n.467+665G>A		intron	N/A
	MYOSLID-AS1	ENST00000417096.5	TSL:4	n.284+665G>A		intron	N/A
	MYOSLID	ENST00000666421.1		n.79-10516C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45403 AN: 151918 Hom.: 6832 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.299 AC: 45429 AN: 152036 Hom.: 6832 Cov.: 32 AF XY: 0.296 AC XY: 22000 AN XY: 74312

African (AFR) AF: 0.285 AC: 11829 AN: 41440

American (AMR) AF: 0.264 AC: 4030 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1362 AN: 3472

East Asian (EAS) AF: 0.283 AC: 1465 AN: 5184

South Asian (SAS) AF: 0.331 AC: 1597 AN: 4818

European-Finnish (FIN) AF: 0.299 AC: 3166 AN: 10572

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20705 AN: 67978

Other (OTH) AF: 0.305 AC: 643 AN: 2106

Alfa AF: 0.246 Hom.: 1103

Bravo AF: 0.295

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		0.091

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs991684;

hg19: chr2-208099497;