rs6732724

Variant names:

• chr2-207180523-G-A
• rs6732724
• ENST00000435643.1:n.181+6709G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-207180523-G-A
• chr2-207180523-G-T

Variant summary

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

The ENST00000435643.1(MYOSLID):​n.181+6709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,868 control chromosomes in the GnomAD database, including 14,632 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 0.43 (14632 hom., cov: 31)
• Consequence: MYOSLID ENST00000435643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 3 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435643.1. 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
	MYOSLID	ENST00000435643.1	TSL:4	n.181+6709G>A		intron	N/A
	MYOSLID	ENST00000666421.1		n.78+14326G>A		intron	N/A
	MYOSLID	ENST00000758487.1		n.65+14326G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64811 AN: 151750 Hom.: 14636 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.427 AC: 64821 AN: 151868 Hom.: 14632 Cov.: 31 AF XY: 0.433 AC XY: 32147 AN XY: 74226

African (AFR) AF: 0.290 AC: 12005 AN: 41418

American (AMR) AF: 0.448 AC: 6842 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1618 AN: 3462

East Asian (EAS) AF: 0.691 AC: 3565 AN: 5160

South Asian (SAS) AF: 0.568 AC: 2732 AN: 4806

European-Finnish (FIN) AF: 0.490 AC: 5154 AN: 10510

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31629 AN: 67912

Other (OTH) AF: 0.414 AC: 875 AN: 2112

Alfa AF: 0.464 Hom.: 8642

Bravo AF: 0.418

Asia WGS AF: 0.621 AC: 2157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.69
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6732724; hg19: chr2-208045247;