6-33339017-T-G

Position:

• chr6-33339017-T-G

Variant summary

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

The ENST00000431574.1(MYL12BP3):​n.40T>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.546 in 1,351,190 control chromosomes in the GnomAD database, including 203,206 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 0.57 (25360 hom., cov: 34)
  • Exomes 𝑓: 0.54 (177846 hom.)
• Consequence: MYL12BP3 ENST00000431574.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.06

Genes affected

MYL12BP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYL12BP3		n.33339017T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYL12BP3	ENST00000431574.1	n.40T>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86946 AN: 152000 Hom.: 25318 Cov.: 34

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.557

GnomAD4 exome AF: 0.543 AC: 651026 AN: 1199072 Hom.: 177846 Cov.: 25 AF XY: 0.547 AC XY: 332895 AN XY: 608582

Gnomad4 AFR exome AF: 0.692

Gnomad4 AMR exome AF: 0.537

Gnomad4 ASJ exome AF: 0.568

Gnomad4 EAS exome AF: 0.374

Gnomad4 SAS exome AF: 0.657

Gnomad4 FIN exome AF: 0.528

Gnomad4 NFE exome AF: 0.534

Gnomad4 OTH exome AF: 0.559

GnomAD4 genome AF: 0.572 AC: 87039 AN: 152118 Hom.: 25360 Cov.: 34 AF XY: 0.573 AC XY: 42616 AN XY: 74366

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.555

Alfa AF: 0.530 Hom.: 32537

Bravo AF: 0.576

Asia WGS AF: 0.527 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130267; hg19: chr6-33306794;