rs6088735

chr20-35157873-C-T

Variant summary

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

The NM_001355008.2(MMP24-AS1-EDEM2):c.-17+7914G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,168 control chromosomes in the GnomAD database, including 4,813 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 0.24 (4813 hom., cov: 32)
• Consequence: MMP24-AS1-EDEM2 NM_001355008.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

MMP24-AS1-EDEM2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMP24-AS1-EDEM2	NM_001355008.2	c.-17+7914G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37079 AN: 152050 Hom.: 4810 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.244 AC: 37105 AN: 152168 Hom.: 4813 Cov.: 32 AF XY: 0.243 AC XY: 18078 AN XY: 74400

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.0331

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.262

Alfa AF: 0.236 Hom.: 4229

Bravo AF: 0.241

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.0
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: rs6088735; hg19: chr20-33745676;