dbSNP rs10819699: NAMA:n.178+24008T>C (chr9-99870872-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+24008T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,884 control chromosomes in the GnomAD database, including 29,446 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 0.61 ( 29446 hom., cov: 31)

Consequence

NAMA
ENST00000655615.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Publications

3 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 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+24008T>C	intron_variant	Intron 2 of 5
NAMA	ENST00000715777.1 link	n.36+24008T>C	intron_variant	Intron 1 of 4
NAMA	ENST00000725618.1 link	n.176+24008T>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

93257

AN:

151766

Hom.:

29407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.536

Gnomad AMI

AF:

0.754

Gnomad AMR

AF:

0.641

Gnomad ASJ

AF:

0.646

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.599

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.691

Gnomad OTH

AF:

0.644

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

GnomAD4 genome

AF:

0.615

AC:

93348

AN:

151884

Hom.:

29446

Cov.:

AF XY:

0.605

AC XY:

44915

AN XY:

74190

show subpopulations

African (AFR)

AF:

0.537

AC:

22237

AN:

41436

American (AMR)

AF:

0.641

AC:

9759

AN:

15220

Ashkenazi Jewish (ASJ)

AF:

0.646

AC:

2242

AN:

3470

East Asian (EAS)

AF:

0.366

AC:

1886

AN:

5148

South Asian (SAS)

AF:

0.367

AC:

1766

AN:

4812

European-Finnish (FIN)

AF:

0.599

AC:

6309

AN:

10538

Middle Eastern (MID)

AF:

0.643

AC:

189

AN:

294

European-Non Finnish (NFE)

AF:

0.691

AC:

46926

AN:

67948

Other (OTH)

AF:

0.639

AC:

1348

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1732

3465

5197

6930

8662

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

768

1536

2304

3072

3840

<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:

0.661

Hom.:

15515

Bravo

AF:

0.619

Asia WGS

AF:

0.396

AC:

1380

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.77

(source)

DANN

Benign

0.48

PhyloP100

-1.1

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over