1-30725886-A-G

Variant names:

• chr1-30725886-A-G
• rs1149048
• ENST00000454613.2:n.1384A>G

Variant summary

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

The ENST00000454613.2(MATN1-AS1):​n.1384A>G 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 0.587 in 152,104 control chromosomes in the GnomAD database, including 28,294 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 0.59 (28270 hom., cov: 31)
  • Exomes 𝑓: 0.51 (24 hom.)
• Consequence: MATN1-AS1 ENST00000454613.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 15 publications found

Genes affected

MATN1-AS1 (HGNC:40364): (MATN1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454613.2. 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
	MATN1-AS1	NR_034182.1		n.1381A>G		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MATN1-AS1	ENST00000454613.2	TSL:1	n.1384A>G		non_coding_transcript_exon	Exon 3 of 4
	MATN1-AS1	ENST00000414532.6	TSL:2	n.3258A>G		non_coding_transcript_exon	Exon 3 of 4
	MATN1-AS1	ENST00000443076.1	TSL:3	n.167A>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89068 AN: 151828 Hom.: 28198 Cov.: 31

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.556

GnomAD4 exome AF: 0.506 AC: 78 AN: 154 Hom.: 24 Cov.: 0 AF XY: 0.434 AC XY: 46 AN XY: 106

African (AFR) AF: 0.875 AC: 7 AN: 8

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 2 AN: 4

South Asian (SAS) AF: 0.500 AC: 11 AN: 22

European-Finnish (FIN) AF: 0.750 AC: 15 AN: 20

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.425 AC: 34 AN: 80

Other (OTH) AF: 0.500 AC: 8 AN: 16

GnomAD4 genome AF: 0.587 AC: 89205 AN: 151950 Hom.: 28270 Cov.: 31 AF XY: 0.585 AC XY: 43471 AN XY: 74252

African (AFR) AF: 0.836 AC: 34673 AN: 41480

American (AMR) AF: 0.607 AC: 9274 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3466

East Asian (EAS) AF: 0.594 AC: 3068 AN: 5164

South Asian (SAS) AF: 0.371 AC: 1786 AN: 4812

European-Finnish (FIN) AF: 0.563 AC: 5927 AN: 10532

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31570 AN: 67894

Other (OTH) AF: 0.554 AC: 1169 AN: 2110

Alfa AF: 0.480 Hom.: 33202

Bravo AF: 0.606

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.042
DANN	Benign	0.52
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1149048;

hg19: chr1-31198733;