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GeneBe

9-99367140-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_102271.1(NAMA):n.1273+521A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,094 control chromosomes in the GnomAD database, including 11,182 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 0.37 ( 11182 hom., cov: 33)

Consequence

NAMA
NR_102271.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0160
Variant links:
Genes affected
NAMA (HGNC:42408): (non-protein coding RNA, associated with MAP kinase pathway and growth arrest)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NAMANR_102271.1 linkuse as main transcriptn.1273+521A>C intron_variant, non_coding_transcript_variant
LOC124902232XR_007061692.1 linkuse as main transcriptn.437-3913T>G intron_variant, non_coding_transcript_variant
NAMANR_102270.1 linkuse as main transcriptn.1410+521A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAMAENST00000604258.5 linkuse as main transcriptn.1380+521A>C intron_variant, non_coding_transcript_variant 1
ENST00000662751.1 linkuse as main transcriptn.433-3913T>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.369
AC:
56074
AN:
151976
Hom.:
11161
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.457
Gnomad AMI
AF:
0.246
Gnomad AMR
AF:
0.457
Gnomad ASJ
AF:
0.259
Gnomad EAS
AF:
0.647
Gnomad SAS
AF:
0.392
Gnomad FIN
AF:
0.382
Gnomad MID
AF:
0.291
Gnomad NFE
AF:
0.279
Gnomad OTH
AF:
0.353
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.369
AC:
56144
AN:
152094
Hom.:
11182
Cov.:
33
AF XY:
0.375
AC XY:
27891
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.457
Gnomad4 AMR
AF:
0.457
Gnomad4 ASJ
AF:
0.259
Gnomad4 EAS
AF:
0.647
Gnomad4 SAS
AF:
0.393
Gnomad4 FIN
AF:
0.382
Gnomad4 NFE
AF:
0.279
Gnomad4 OTH
AF:
0.359
Alfa
AF:
0.329
Hom.:
1102
Bravo
AF:
0.382
Asia WGS
AF:
0.579
AC:
2015
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
4.7
Dann
Benign
0.47

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1555573; hg19: chr9-102129422; API