9-123589939-G-A

Variant names:

• chr9-123589939-G-A
• rs7852296
• NM_001352964.2:c.766-6669C>T

Variant summary

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

The NM_001352964.2(DENND1A):​c.766-6669C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,248 control chromosomes in the GnomAD database, including 999 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 0.11 (999 hom., cov: 32)
• Consequence: DENND1A NM_001352964.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352964.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DENND1A	NM_001352964.2	MANE Select	c.766-6669C>T		intron	N/A	NP_001339893.1
	DENND1A	NM_001393654.1		c.766-6669C>T		intron	N/A	NP_001380583.1
	DENND1A	NM_001352965.2		c.670-6669C>T		intron	N/A	NP_001339894.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DENND1A	ENST00000394215.7	TSL:5 MANE Select	c.766-6669C>T		intron	N/A	ENSP00000377763.4
	DENND1A	ENST00000373620.7	TSL:1	c.766-6669C>T		intron	N/A	ENSP00000362722.3
	DENND1A	ENST00000373618.1	TSL:1	c.670-6669C>T		intron	N/A	ENSP00000362720.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16428 AN: 152130 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.0893

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0928

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.108 AC: 16472 AN: 152248 Hom.: 999 Cov.: 32 AF XY: 0.108 AC XY: 8027 AN XY: 74428

African (AFR) AF: 0.150 AC: 6236 AN: 41524

American (AMR) AF: 0.0890 AC: 1361 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 320 AN: 3472

East Asian (EAS) AF: 0.0890 AC: 461 AN: 5182

South Asian (SAS) AF: 0.139 AC: 672 AN: 4826

European-Finnish (FIN) AF: 0.0713 AC: 755 AN: 10596

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0928 AC: 6314 AN: 68028

Other (OTH) AF: 0.108 AC: 229 AN: 2116

Alfa AF: 0.0996 Hom.: 2138

Bravo AF: 0.111

Asia WGS AF: 0.107 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.26
PhyloP100		0.19
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: rs7852296; hg19: chr9-126352218;