chr5-89301402-G-A

Position:

• chr5-89301402-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000692568.1(ENSG00000288740):​n.1688C>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 0.02 in 152,044 control chromosomes in the GnomAD database, including 40 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 0.020 (40 hom., cov: 32)
• Consequence: ENST00000692568.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

Genes affected

(HGNC:):

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=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.02 (3048/152044) while in subpopulation NFE AF= 0.0309 (2100/67910). AF 95% confidence interval is 0.0298. There are 40 homozygotes in gnomad4. There are 1486 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 40 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEF2C-AS1	NR_136218.1	n.535-75881G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692568.1	n.1688C>T		non_coding_transcript_exon_variant	1/1
MEF2C-AS1	ENST00000514092.5	n.245-75881G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0201 AC: 3051 AN: 151926 Hom.: 40 Cov.: 32

Gnomad AFR AF: 0.00526

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00911

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0200 AC: 3048 AN: 152044 Hom.: 40 Cov.: 32 AF XY: 0.0200 AC XY: 1486 AN XY: 74338

Gnomad4 AFR AF: 0.00522

Gnomad4 AMR AF: 0.0186

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00911

Gnomad4 FIN AF: 0.0273

Gnomad4 NFE AF: 0.0309

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.0251 Hom.: 10

Bravo AF: 0.0181

Asia WGS AF: 0.00375 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.048
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1895217; hg19: chr5-88597219;