rs6060269

Positions:

• chr20-35148712-C-A
• chr20-35148712-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.-16-1777G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.17 (385 hom., cov: 0)
• Consequence: MMP24-AS1-EDEM2 NM_001355008.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMP24-AS1-EDEM2	NM_001355008.2	c.-16-1777G>T		intron_variant			NP_001341937.1
		n.35148712C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.169 AC: 3295 AN: 19448 Hom.: 380 Cov.: 0

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.0984

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.281

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.170 AC: 3319 AN: 19494 Hom.: 385 Cov.: 0 AF XY: 0.188 AC XY: 1770 AN XY: 9408

Gnomad4 AFR AF: 0.0897

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.10
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6060269; hg19: chr20-33736515;