Genetic Variant ENST00000454613.2:n.1384A>G (chr1-30725886-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.24

Publications

15 publications found

Variant links:

Genes affected

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

MATN1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MATN1-AS1	NR_034182.1 link	n.1381A>G		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MATN1-AS1	ENST00000454613.2 link	n.1384A>G	non_coding_transcript_exon_variant	Exon 3 of 4	1
MATN1-AS1	ENST00000414532.6 link	n.3258A>G	non_coding_transcript_exon_variant	Exon 3 of 4	2
MATN1-AS1	ENST00000443076.1 link	n.167A>G	non_coding_transcript_exon_variant	Exon 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.587

AC:

89068

AN:

151828

Hom.:

28198

Cov.:

show subpopulations

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:

AN:

154

Hom.:

Cov.:

AF XY:

0.434

AC XY:

AN XY:

106

show subpopulations

African (AFR)

AF:

0.875

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.425

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.587

AC:

89205

AN:

151950

Hom.:

28270

Cov.:

AF XY:

0.585

AC XY:

43471

AN XY:

74252

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

1734

3469

5203

6938

8672

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.042

(source)

DANN

Benign

0.52

PhyloP100

-2.2

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over