rs2479104

Variant names:

• chr9-123822822-T-C
• rs2479104
• NM_001352964.2:c.89-30192A>G

Variant summary

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

The NM_001352964.2(DENND1A):​c.89-30192A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,194 control chromosomes in the GnomAD database, including 9,071 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 0.26 (9071 hom., cov: 32)
• Consequence: DENND1A NM_001352964.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 3 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DENND1A	NM_001352964.2	c.89-30192A>G		intron_variant	Intron 2 of 23	ENST00000394215.7	NP_001339893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DENND1A	ENST00000394215.7	c.89-30192A>G		intron_variant	Intron 2 of 23	5	NM_001352964.2	ENSP00000377763.4
DENND1A	ENST00000373620.7	c.89-30192A>G		intron_variant	Intron 2 of 20	1		ENSP00000362722.3
DENND1A	ENST00000373618.1	c.43-30192A>G		intron_variant	Intron 2 of 18	1		ENSP00000362720.1
DENND1A	ENST00000373624.6	c.89-30192A>G		intron_variant	Intron 2 of 21	5		ENSP00000362727.2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38880 AN: 152076 Hom.: 9041 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0643

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.256 AC: 38957 AN: 152194 Hom.: 9071 Cov.: 32 AF XY: 0.252 AC XY: 18771 AN XY: 74416

African (AFR) AF: 0.624 AC: 25878 AN: 41478

American (AMR) AF: 0.136 AC: 2079 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 529 AN: 3470

East Asian (EAS) AF: 0.0643 AC: 333 AN: 5182

South Asian (SAS) AF: 0.186 AC: 899 AN: 4826

European-Finnish (FIN) AF: 0.0998 AC: 1060 AN: 10616

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7559 AN: 68000

Other (OTH) AF: 0.229 AC: 484 AN: 2114

Alfa AF: 0.153 Hom.: 1569

Bravo AF: 0.274

Asia WGS AF: 0.139 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.92
DANN	Benign	0.54
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2479104; hg19: chr9-126585101;