rs6088735

Variant names:

• chr20-35157873-C-T
• rs6088735
• NM_001355008.2:c.-17+7914G>A

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+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
• Publications: 30 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355008.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMP24-AS1-EDEM2	NM_001355008.2		c.-17+7914G>A		intron	N/A	NP_001341937.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.311 AC: 12923 AN: 41514

American (AMR) AF: 0.192 AC: 2938 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1105 AN: 3472

East Asian (EAS) AF: 0.0331 AC: 172 AN: 5190

South Asian (SAS) AF: 0.266 AC: 1285 AN: 4828

European-Finnish (FIN) AF: 0.258 AC: 2731 AN: 10582

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15045 AN: 68002

Other (OTH) AF: 0.262 AC: 551 AN: 2104

Alfa AF: 0.231 Hom.: 12719

Bravo AF: 0.241

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.0
DANN	Benign	0.79
PhyloP100		0.15
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: rs6088735; hg19: chr20-33745676;