rs6088738

chr20-35159528-G-Achr20-35159528-G-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+6259C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,948 control chromosomes in the GnomAD database, including 5,319 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 (5319 hom., cov: 31)
• Consequence: MMP24-AS1-EDEM2 NM_001355008.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMP24-AS1-EDEM2	NM_001355008.2	c.-17+6259C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38738 AN: 151830 Hom.: 5313 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.0332

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.363

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: 0.255 AC: 38769 AN: 151948 Hom.: 5319 Cov.: 31 AF XY: 0.254 AC XY: 18843 AN XY: 74270

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.0333

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.276

Alfa AF: 0.172 Hom.: 501

Bravo AF: 0.255

Asia WGS AF: 0.211 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.2
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6088738; hg19: chr20-33747331;