rs11684598

Positions:

• chr2-33727554-G-A

Variant summary

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

The ENST00000490394.1(MYADML):​n.11C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 1,271,480 control chromosomes in the GnomAD database, including 139,827 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 0.46 (16271 hom., cov: 33)
  • Exomes 𝑓: 0.47 (123556 hom.)
• Consequence: MYADML ENST00000490394.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.929

Genes affected

MYADML (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYADML	NR_003143.2	n.664C>T		non_coding_transcript_exon_variant	1/1
LINC01317	NR_126403.1	n.68+20601G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYADML	ENST00000474610.1	n.654C>T		non_coding_transcript_exon_variant	1/1	6
MYADML	ENST00000490394.1	n.11C>T		non_coding_transcript_exon_variant	1/3	3
MYADML	ENST00000491596.1	n.435C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69176 AN: 151914 Hom.: 16267 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.432

GnomAD3 exomes AF: 0.488 AC: 115834 AN: 237342 Hom.: 28689 AF XY: 0.488 AC XY: 63072 AN XY: 129358

Gnomad AFR exome AF: 0.338

Gnomad AMR exome AF: 0.588

Gnomad ASJ exome AF: 0.404

Gnomad EAS exome AF: 0.433

Gnomad SAS exome AF: 0.480

Gnomad FIN exome AF: 0.531

Gnomad NFE exome AF: 0.493

Gnomad OTH exome AF: 0.472

GnomAD4 exome AF: 0.468 AC: 523375 AN: 1119448 Hom.: 123556 Cov.: 19 AF XY: 0.469 AC XY: 268042 AN XY: 571532

Gnomad4 AFR exome AF: 0.317

Gnomad4 AMR exome AF: 0.581

Gnomad4 ASJ exome AF: 0.398

Gnomad4 EAS exome AF: 0.461

Gnomad4 SAS exome AF: 0.475

Gnomad4 FIN exome AF: 0.525

Gnomad4 NFE exome AF: 0.467

Gnomad4 OTH exome AF: 0.452

GnomAD4 genome AF: 0.455 AC: 69203 AN: 152032 Hom.: 16271 Cov.: 33 AF XY: 0.461 AC XY: 34248 AN XY: 74304

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.435

Alfa AF: 0.478 Hom.: 15812

Bravo AF: 0.446

Asia WGS AF: 0.437 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	0.36
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11684598; hg19: chr2-33952621;