rs6060278

Variant names:

• chr20-35165459-T-C
• rs6060278
• NM_001355008.2:c.-17+328A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 publications found

Genes affected

MMP24-AS1-EDEM2 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MMP24-AS1-EDEM2	NM_001355008.2	c.-17+328A>G		intron_variant	Intron 5 of 14		NP_001341937.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.355 AC: 14607 AN: 41108

American (AMR) AF: 0.203 AC: 3063 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3464

East Asian (EAS) AF: 0.0341 AC: 175 AN: 5128

South Asian (SAS) AF: 0.267 AC: 1270 AN: 4752

European-Finnish (FIN) AF: 0.259 AC: 2689 AN: 10392

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15014 AN: 67794

Other (OTH) AF: 0.276 AC: 578 AN: 2098

Alfa AF: 0.233 Hom.: 14992

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
PhyloP100		-0.68
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6060278; hg19: chr20-33753262;