5-39429414-C-G

Variant names:

• chr5-39429414-C-G
• rs1025048
• ENST00000511792.5:c.-102+32664G>C

Variant summary

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

The ENST00000511792.5(DAB2):​c.-102+32664G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,928 control chromosomes in the GnomAD database, including 9,955 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 0.34 (9955 hom., cov: 32)
• Consequence: DAB2 ENST00000511792.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 3 publications found

Genes affected

DAB2 (HGNC:2662): (DAB adaptor protein 2) This gene encodes a mitogen-responsive phosphoprotein. It is expressed in normal ovarian epithelial cells, but is down-regulated or absent from ovarian carcinoma cell lines, suggesting its role as a tumor suppressor. This protein binds to the SH3 domains of GRB2, an adaptor protein that couples tyrosine kinase receptors to SOS (a guanine nucleotide exchange factor for Ras), via its C-terminal proline-rich sequences, and may thus modulate growth factor/Ras pathways by competing with SOS for binding to GRB2. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAB2	ENST00000511792.5	c.-102+32664G>C		intron_variant	Intron 1 of 2	4		ENSP00000427541.1
DAB2	ENST00000509457.1	n.78-11069G>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52315 AN: 151812 Hom.: 9943 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.345 AC: 52356 AN: 151928 Hom.: 9955 Cov.: 32 AF XY: 0.341 AC XY: 25281 AN XY: 74238

African (AFR) AF: 0.513 AC: 21259 AN: 41406

American (AMR) AF: 0.215 AC: 3290 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1113 AN: 5160

South Asian (SAS) AF: 0.274 AC: 1319 AN: 4816

European-Finnish (FIN) AF: 0.363 AC: 3832 AN: 10546

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19667 AN: 67948

Other (OTH) AF: 0.305 AC: 643 AN: 2106

Alfa AF: 0.175 Hom.: 330

Bravo AF: 0.342

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1025048; hg19: chr5-39429516;