chr5-89301402-G-A

Variant names:

• chr5-89301402-G-A
• rs1895217
• ENST00000686965.1:n.638C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000686965.1(ENSG00000288740):​n.638C>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: ENSG00000288740 ENST00000686965.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 0 publications found

Genes affected

ENSG00000288740 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 40 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000686965.1. 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
	MEF2C-AS1	NR_136217.1		n.382-75881G>A		intron	N/A
	MEF2C-AS1	NR_136218.1		n.535-75881G>A		intron	N/A
	MEF2C-AS1	NR_136219.1		n.568-75881G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288740	ENST00000686965.1		n.638C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000288740	ENST00000692568.1		n.1688C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288740	ENST00000693054.2		n.542C>T		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.00522 AC: 217 AN: 41536

American (AMR) AF: 0.0186 AC: 283 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.00911 AC: 44 AN: 4828

European-Finnish (FIN) AF: 0.0273 AC: 290 AN: 10604

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0309 AC: 2100 AN: 67910

Other (OTH) AF: 0.0199 AC: 42 AN: 2110

Alfa AF: 0.0284 Hom.: 115

Bravo AF: 0.0181

Asia WGS AF: 0.00375 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.048
DANN	Benign	0.79
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1895217; hg19: chr5-88597219;