19-50501497-A-G

Variant names:

• chr19-50501497-A-G
• rs1298062
• ENST00000702920.2:n.152+366T>C

Variant summary

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

The ENST00000702920.2(MYREM):​n.152+366T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,096 control chromosomes in the GnomAD database, including 44,288 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 0.76 (44288 hom., cov: 34)
• Consequence: MYREM ENST00000702920.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 11 publications found

Genes affected

MYREM (HGNC:56685): (MYBPC2 cis regulating lncRNA enhancer of myogenesis)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702920.2. 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
	MYREM	ENST00000702920.2		n.152+366T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114864 AN: 151978 Hom.: 44227 Cov.: 34

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.756 AC: 114982 AN: 152096 Hom.: 44288 Cov.: 34 AF XY: 0.757 AC XY: 56249 AN XY: 74332

African (AFR) AF: 0.918 AC: 38132 AN: 41520

American (AMR) AF: 0.779 AC: 11915 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2344 AN: 3468

East Asian (EAS) AF: 0.697 AC: 3587 AN: 5150

South Asian (SAS) AF: 0.755 AC: 3648 AN: 4830

European-Finnish (FIN) AF: 0.667 AC: 7064 AN: 10588

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45753 AN: 67930

Other (OTH) AF: 0.766 AC: 1613 AN: 2106

Alfa AF: 0.698 Hom.: 141598

Bravo AF: 0.769

Asia WGS AF: 0.742 AC: 2583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.26
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1298062; hg19: chr19-51004754;