rs11759513

Positions:

• chr6-11198581-G-A
• chr6-11198581-G-C
• chr6-11198581-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000379433.5(NEDD9):​c.*2400C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,106 control chromosomes in the GnomAD database, including 6,717 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 0.27 (6716 hom., cov: 32)
  • Exomes 𝑓: 0.28 (1 hom.)
• Consequence: NEDD9 ENST00000379433.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEDD9	NM_006403.4	c.460-4889C>T		intron_variant		ENST00000379446.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEDD9	ENST00000379446.10	c.460-4889C>T		intron_variant		1	NM_006403.4	P4
	ENST00000500636.2	n.176-8880G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40847 AN: 151956 Hom.: 6719 Cov.: 32

Gnomad AFR AF: 0.0839

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.281 AC: 9 AN: 32 Hom.: 1 Cov.: 0 AF XY: 0.350 AC XY: 7 AN XY: 20

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.269 AC: 40842 AN: 152074 Hom.: 6716 Cov.: 32 AF XY: 0.278 AC XY: 20642 AN XY: 74334

Gnomad4 AFR AF: 0.0838

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.295

Alfa AF: 0.248 Hom.: 1305

Bravo AF: 0.259

Asia WGS AF: 0.471 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11759513; hg19: chr6-11198814;