Genetic Variant NAMA:n.507+13511A>G (chr9-99377245-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000715772.1(NAMA):n.507+13511A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,980 control chromosomes in the GnomAD database, including 30,225 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 0.62 ( 30212 hom., cov: 31)

Exomes 𝑓: 0.71 ( 13 hom. )

Consequence

NAMA
ENST00000715772.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.314

Publications

8 publications found

Variant links:

Genes affected

NAMA (HGNC:42408): (non-protein coding RNA, associated with MAP kinase pathway and growth arrest)

NAMA links:

ENSG00000287955 (HGNC:):

ENSG00000287955 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
NAMA	ENST00000715772.1 link	n.507+13511A>G	intron_variant	Intron 5 of 5
NAMA	ENST00000725614.1 link	n.401-21663A>G	intron_variant	Intron 4 of 4
NAMA	ENST00000725645.1 link	n.111-21643A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.618

AC:

93795

AN:

151822

Hom.:

30213

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.757

Gnomad AMR

AF:

0.538

Gnomad ASJ

AF:

0.745

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.643

Gnomad FIN

AF:

0.618

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.729

Gnomad OTH

AF:

0.643

GnomAD4 exome

AF:

0.714

AC:

AN:

Hom.:

Cov.:

AF XY:

0.714

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.617

AC:

93817

AN:

151938

Hom.:

30212

Cov.:

AF XY:

0.612

AC XY:

45466

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.479

AC:

19835

AN:

41398

American (AMR)

AF:

0.538

AC:

8214

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.745

AC:

2586

AN:

3472

East Asian (EAS)

AF:

0.356

AC:

1834

AN:

5156

South Asian (SAS)

AF:

0.643

AC:

3092

AN:

4810

European-Finnish (FIN)

AF:

0.618

AC:

6521

AN:

10554

Middle Eastern (MID)

AF:

0.677

AC:

199

AN:

294

European-Non Finnish (NFE)

AF:

0.728

AC:

49504

AN:

67956

Other (OTH)

AF:

0.637

AC:

1342

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1696

3392

5088

6784

8480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

764

1528

2292

3056

3820

<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:

0.691

Hom.:

97116

Bravo

AF:

0.602

Asia WGS

AF:

0.433

AC:

1509

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

0.31

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