dbSNP rs12686676: NAMA:n.178+24669T>C (chr9-99870211-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 ENST00000655615.1(NAMA):n.178+24669T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,948 control chromosomes in the GnomAD database, including 16,673 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 0.45 ( 16673 hom., cov: 30)

Consequence

NAMA
ENST00000655615.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.729

Publications

9 publications found

Variant links:

Genes affected

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

NAMA 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 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	ENST00000655615.1 link	n.178+24669T>C	intron_variant	Intron 2 of 5
NAMA	ENST00000715777.1 link	n.36+24669T>C	intron_variant	Intron 1 of 4
NAMA	ENST00000725618.1 link	n.176+24669T>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.452

AC:

68669

AN:

151830

Hom.:

16666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.611

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.361

Gnomad SAS

AF:

0.277

Gnomad FIN

AF:

0.467

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.558

Gnomad OTH

AF:

0.492

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.452

AC:

68688

AN:

151948

Hom.:

16673

Cov.:

AF XY:

0.443

AC XY:

32905

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.302

AC:

12513

AN:

41434

American (AMR)

AF:

0.425

AC:

6491

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.541

AC:

1874

AN:

3464

East Asian (EAS)

AF:

0.361

AC:

1866

AN:

5166

South Asian (SAS)

AF:

0.280

AC:

1348

AN:

4812

European-Finnish (FIN)

AF:

0.467

AC:

4929

AN:

10560

Middle Eastern (MID)

AF:

0.548

AC:

161

AN:

294

European-Non Finnish (NFE)

AF:

0.558

AC:

37923

AN:

67940

Other (OTH)

AF:

0.486

AC:

1029

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1832

3664

5496

7328

9160

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

628

1256

1884

2512

3140

<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:

0.373

Hom.:

1081

Bravo

AF:

0.448

Asia WGS

AF:

0.324

AC:

1129

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

0.73

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over