20-35165459-T-C

Position:

• chr20-35165459-T-C

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+328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,040 control chromosomes in the GnomAD database, including 5,377 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 0.26 (5377 hom., cov: 29)
• Consequence: MMP24-AS1-EDEM2 NM_001355008.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMP24-AS1-EDEM2	NM_001355008.2	c.-17+328A>G		intron_variant			NP_001341937.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38814 AN: 150922 Hom.: 5373 Cov.: 29

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.257 AC: 38847 AN: 151040 Hom.: 5377 Cov.: 29 AF XY: 0.256 AC XY: 18843 AN XY: 73724

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.0341

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.276

Alfa AF: 0.230 Hom.: 5821

Bravo AF: 0.257

Asia WGS AF: 0.213 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6060278; hg19: chr20-33753262;