5-89031965-T-G

Position:

• chr5-89031965-T-G

Variant summary

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

The NR_136218.1(MEF2C-AS1):​n.401-62994T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,002 control chromosomes in the GnomAD database, including 25,672 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 0.56 (25672 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: MEF2C-AS1 NR_136218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

Genes affected

MEF2C-AS1 (HGNC:48908): (MEF2C antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEF2C-AS1	NR_136218.1	n.401-62994T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEF2C-AS1	ENST00000514092.5	n.174-62994T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85285 AN: 151884 Hom.: 25602 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.551

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.562 AC: 85416 AN: 152002 Hom.: 25672 Cov.: 32 AF XY: 0.557 AC XY: 41357 AN XY: 74310

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.555

Alfa AF: 0.486 Hom.: 9121

Bravo AF: 0.586

Asia WGS AF: 0.509 AC: 1763 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6894139; hg19: chr5-88327782;