rs16871204

Variant names:

• chr6-11277292-T-C
• rs16871204
• ENST00000448183.6:n.106+27774A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142393.2(NEDD9):​c.12+28700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 152,224 control chromosomes in the GnomAD database, including 379 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 0.069 (379 hom., cov: 32)
• Consequence: NEDD9 NM_001142393.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142393.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEDD9	NM_001142393.2		c.12+28700A>G		intron	N/A	NP_001135865.1	Q14511-3
	NEDD9	NR_073131.1		n.468+27774A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEDD9	ENST00000448183.6	TSL:1	n.106+27774A>G		intron	N/A	ENSP00000395237.2	D6RDV1
	NEDD9	ENST00000504387.5	TSL:2	c.12+28700A>G		intron	N/A	ENSP00000422871.1	Q14511-3
	NEDD9	ENST00000397378.7	TSL:3	c.12+28700A>G		intron	N/A	ENSP00000380534.3	D6RBQ2

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10538 AN: 152106 Hom.: 375 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.0453

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0693 AC: 10551 AN: 152224 Hom.: 379 Cov.: 32 AF XY: 0.0701 AC XY: 5218 AN XY: 74432

African (AFR) AF: 0.104 AC: 4305 AN: 41516

American (AMR) AF: 0.0666 AC: 1019 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3470

East Asian (EAS) AF: 0.0418 AC: 217 AN: 5186

South Asian (SAS) AF: 0.0458 AC: 221 AN: 4828

European-Finnish (FIN) AF: 0.0606 AC: 642 AN: 10596

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0549 AC: 3731 AN: 68014

Other (OTH) AF: 0.0747 AC: 158 AN: 2116

Alfa AF: 0.0630 Hom.: 131

Bravo AF: 0.0730

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.9
DANN	Benign	0.78
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs16871204; hg19: chr6-11277525;