1-30725886-A-G

Position:

• chr1-30725886-A-G

Variant summary

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

The ENST00000454613.1(MATN1-AS1):​n.1381A>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 ENST00000454613.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

Genes affected

MATN1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MATN1-AS1	NR_034182.1	n.1381A>G		non_coding_transcript_exon_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MATN1-AS1	ENST00000454613.1	n.1381A>G		non_coding_transcript_exon_variant	3/4	1
MATN1-AS1	ENST00000414532.6	n.3258A>G		non_coding_transcript_exon_variant	3/4	2
MATN1-AS1	ENST00000443076.1	n.167A>G		non_coding_transcript_exon_variant	1/2	3

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

Gnomad4 AFR exome AF: 0.875

Gnomad4 AMR exome AF: 0.250

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.425

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.554

Alfa AF: 0.464 Hom.: 19287

Bravo AF: 0.606

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1149048; hg19: chr1-31198733;