rs16871188

Variant names:

• chr6-11272324-A-G
• rs16871188
• ENST00000448183.6:n.106+32742T>C

Variant summary

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

The ENST00000448183.6(NEDD9):​n.106+32742T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,290 control chromosomes in the GnomAD database, including 600 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 (600 hom., cov: 32)
• Consequence: NEDD9 ENST00000448183.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEDD9	NM_001142393.2	c.12+33668T>C		intron_variant	Intron 2 of 7		NP_001135865.1
NEDD9	NR_073131.1	n.468+32742T>C		intron_variant	Intron 3 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEDD9	ENST00000448183.6	n.106+32742T>C		intron_variant	Intron 3 of 9	1		ENSP00000395237.2
NEDD9	ENST00000504387.5	c.12+33668T>C		intron_variant	Intron 2 of 7	2		ENSP00000422871.1
NEDD9	ENST00000397378.7	c.12+33668T>C		intron_variant	Intron 3 of 3	3		ENSP00000380534.3

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 12456 AN: 152172 Hom.: 594 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.0407

Gnomad SAS AF: 0.0453

Gnomad FIN AF: 0.0604

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0819 AC: 12480 AN: 152290 Hom.: 600 Cov.: 32 AF XY: 0.0820 AC XY: 6103 AN XY: 74458

African (AFR) AF: 0.146 AC: 6071 AN: 41536

American (AMR) AF: 0.0752 AC: 1151 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3470

East Asian (EAS) AF: 0.0406 AC: 211 AN: 5192

South Asian (SAS) AF: 0.0457 AC: 221 AN: 4832

European-Finnish (FIN) AF: 0.0604 AC: 641 AN: 10618

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0551 AC: 3746 AN: 68016

Other (OTH) AF: 0.0856 AC: 181 AN: 2114

Alfa AF: 0.0701 Hom.: 89

Bravo AF: 0.0872

Asia WGS AF: 0.0610 AC: 214 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	2.8
DANN	Benign	0.42
PhyloP100		0.085
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: rs16871188; hg19: chr6-11272557;