6-11271759-T-C

Variant summary

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

The NM_001142393.2(NEDD9):​c.12+34233A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,298 control chromosomes in the GnomAD database, including 593 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 0.082 ( 593 hom., cov: 32)
Exomes 𝑓: 0.063 ( 0 hom. )

Consequence

NEDD9
NM_001142393.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.439
Variant links:
Genes affected
NEDD9 (HGNC:7733): (neural precursor cell expressed, developmentally down-regulated 9) The protein encoded by this gene is a member of the CRK-associated substrates family. Members of this family are adhesion docking molecules that mediate protein-protein interactions for signal transduction pathways. This protein is a focal adhesion protein that acts as a scaffold to regulate signaling complexes important in cell attachment, migration and invasion as well as apoptosis and the cell cycle. This protein has also been reported to have a role in cancer metastasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NEDD9NM_001142393.2 linkc.12+34233A>G intron_variant Intron 2 of 7 NP_001135865.1 Q14511-3A0A024QZV9
NEDD9NR_073131.1 linkn.468+33307A>G intron_variant Intron 3 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NEDD9ENST00000448183.6 linkn.106+33307A>G intron_variant Intron 3 of 9 1 ENSP00000395237.2 D6RDV1
NEDD9ENST00000504387.5 linkc.12+34233A>G intron_variant Intron 2 of 7 2 ENSP00000422871.1 Q14511-3
NEDD9ENST00000397378.7 linkc.12+34233A>G intron_variant Intron 3 of 3 3 ENSP00000380534.3 D6RBQ2

Frequencies

GnomAD3 genomes
AF:
0.0816
AC:
12423
AN:
152166
Hom.:
587
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.145
Gnomad AMI
AF:
0.0143
Gnomad AMR
AF:
0.0749
Gnomad ASJ
AF:
0.0585
Gnomad EAS
AF:
0.0423
Gnomad SAS
AF:
0.0453
Gnomad FIN
AF:
0.0604
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.0550
Gnomad OTH
AF:
0.0869
GnomAD4 exome
AF:
0.0625
AC:
1
AN:
16
Hom.:
0
Cov.:
0
AF XY:
0.0833
AC XY:
1
AN XY:
12
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0833
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0817
AC:
12447
AN:
152282
Hom.:
593
Cov.:
32
AF XY:
0.0818
AC XY:
6095
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.145
Gnomad4 AMR
AF:
0.0748
Gnomad4 ASJ
AF:
0.0585
Gnomad4 EAS
AF:
0.0422
Gnomad4 SAS
AF:
0.0458
Gnomad4 FIN
AF:
0.0604
Gnomad4 NFE
AF:
0.0551
Gnomad4 OTH
AF:
0.0860
Alfa
AF:
0.0364
Hom.:
34
Bravo
AF:
0.0870
Asia WGS
AF:
0.0610
AC:
213
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
2.0
DANN
Benign
0.48

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: rs16871186; hg19: chr6-11271992; API