chr16-3044260-G-A

Variant names:

• chr16-3044260-G-A
• rs1004792
• ENST00000722320.1:n.942C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000722320.1(MMP25-AS1):​n.942C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,808 control chromosomes in the GnomAD database, including 3,638 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 0.21 (3638 hom., cov: 31)
• Consequence: MMP25-AS1 ENST00000722320.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 11 publications found

Genes affected

MMP25-AS1 (HGNC:51372): (MMP25 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722320.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMP25-AS1	ENST00000722320.1		n.942C>T		non_coding_transcript_exon	Exon 3 of 3
	MMP25-AS1	ENST00000722321.1		n.481C>T		non_coding_transcript_exon	Exon 2 of 2
	MMP25-AS1	ENST00000576250.6	TSL:5	n.1111-5166C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32331 AN: 151688 Hom.: 3636 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.213 AC: 32356 AN: 151808 Hom.: 3638 Cov.: 31 AF XY: 0.216 AC XY: 16022 AN XY: 74182

African (AFR) AF: 0.142 AC: 5896 AN: 41394

American (AMR) AF: 0.200 AC: 3046 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3466

East Asian (EAS) AF: 0.117 AC: 603 AN: 5146

South Asian (SAS) AF: 0.243 AC: 1168 AN: 4806

European-Finnish (FIN) AF: 0.304 AC: 3197 AN: 10524

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17130 AN: 67928

Other (OTH) AF: 0.203 AC: 428 AN: 2110

Alfa AF: 0.232 Hom.: 16224

Bravo AF: 0.198

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.42
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1004792; hg19: chr16-3094261;