rs1004792

Positions:

• chr16-3044260-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000576250.6(MMP25-AS1):​n.1111-5166C>T variant causes a intron, non coding transcript 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 ENST00000576250.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMP25-AS1	ENST00000576250.6	n.1111-5166C>T		intron_variant, non_coding_transcript_variant		5
MMP25-AS1	ENST00000649784.1	n.2305-1649C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.203

Alfa AF: 0.237 Hom.: 6976

Bravo AF: 0.198

Asia WGS AF: 0.183 AC: 636 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	2.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1004792; hg19: chr16-3094261;