rs10818814

Positions:

• chr9-123398694-A-T

Variant summary

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

The NM_001352964.2(DENND1A):​c.1631+4708T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 149,876 control chromosomes in the GnomAD database, including 13,961 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 0.39 (13961 hom., cov: 31)
• Consequence: DENND1A NM_001352964.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943

Genes affected

DENND1A (HGNC:29324): (DENN domain containing 1A) Clathrin (see MIM 118955)-mediated endocytosis is a major mechanism for internalization of proteins and lipids. Members of the connecdenn family, such as DENND1A, function as guanine nucleotide exchange factors (GEFs) for the early endosomal small GTPase RAB35 (MIM 604199) and bind to clathrin and clathrin adaptor protein-2 (AP2; see MIM 601024). Thus, connecdenns link RAB35 activation with the clathrin machinery (Marat and McPherson, 2010 [PubMed 20154091]).[supplied by OMIM, Nov 2010]

DENND1A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DENND1A	NM_001352964.2	c.1631+4708T>A		intron_variant		ENST00000394215.7	NP_001339893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DENND1A	ENST00000394215.7	c.1631+4708T>A		intron_variant		5	NM_001352964.2	ENSP00000377763.4
DENND1A	ENST00000473039.5	n.1440+4708T>A		intron_variant		1
DENND1A	ENST00000373624.6	c.1577+4708T>A		intron_variant		5		ENSP00000362727.2

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59015 AN: 149762 Hom.: 13969 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.394 AC: 58984 AN: 149876 Hom.: 13961 Cov.: 31 AF XY: 0.391 AC XY: 28645 AN XY: 73170

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.418

Alfa AF: 0.455 Hom.: 2238

Bravo AF: 0.365

Asia WGS AF: 0.313 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.83

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: rs10818814; hg19: chr9-126160973;