dbSNP rs35775808: NAMA:n.231-190T>C (chr9-99463262-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 ENST00000652827.1(NAMA):n.231-190T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0445 in 152,302 control chromosomes in the GnomAD database, including 212 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 0.045 ( 212 hom., cov: 32)

Consequence

NAMA
ENST00000652827.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.750

Publications

5 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0631 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	ENST00000652827.1 link	n.231-190T>C	intron_variant	Intron 2 of 5
NAMA	ENST00000655615.1 link	n.269-190T>C	intron_variant	Intron 3 of 5
NAMA	ENST00000715772.1 link	n.281-63614T>C	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.0446

AC:

6785

AN:

152184

Hom.:

212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0125

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.0388

Gnomad ASJ

AF:

0.0545

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0354

Gnomad FIN

AF:

0.0731

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0647

Gnomad OTH

AF:

0.0406

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

GnomAD4 genome

AF:

0.0445

AC:

6784

AN:

152302

Hom.:

212

Cov.:

AF XY:

0.0450

AC XY:

3348

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.0125

AC:

520

AN:

41578

American (AMR)

AF:

0.0387

AC:

593

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0545

AC:

189

AN:

3470

East Asian (EAS)

AF:

0.00135

AC:

AN:

5176

South Asian (SAS)

AF:

0.0355

AC:

171

AN:

4820

European-Finnish (FIN)

AF:

0.0731

AC:

776

AN:

10614

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0647

AC:

4399

AN:

68012

Other (OTH)

AF:

0.0402

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

332

663

995

1326

1658

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

228

304

380

<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:

0.0443

Hom.:

114

Bravo

AF:

0.0410

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.0

(source)

DANN

Benign

0.71

PhyloP100

0.75

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