6-11238791-A-G

Position:

• chr6-11238791-A-G

Variant summary

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

The NM_001142393.2(NEDD9):​c.13-25064T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,028 control chromosomes in the GnomAD database, including 21,492 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 0.53 (21492 hom., cov: 32)
• Consequence: NEDD9 NM_001142393.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

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]

ENSG00000247925 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NEDD9	NM_001142393.2	c.13-25064T>C		intron_variant			NP_001135865.1
NEDD9	NR_073131.1	n.469-25064T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEDD9	ENST00000448183.6	n.107-25064T>C		intron_variant		1		ENSP00000395237.2
NEDD9	ENST00000504387.5	c.13-25064T>C		intron_variant		2		ENSP00000422871.1
NEDD9	ENST00000397378.7	c.13-25064T>C		intron_variant		3		ENSP00000380534.3

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80508 AN: 151912 Hom.: 21472 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.530 AC: 80572 AN: 152028 Hom.: 21492 Cov.: 32 AF XY: 0.529 AC XY: 39283 AN XY: 74294

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.540

Alfa AF: 0.525 Hom.: 17605

Bravo AF: 0.523

Asia WGS AF: 0.535 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6457160; hg19: chr6-11239024;