rs13231650

Variant names:

• chr7-141699142-T-C
• rs13231650
• NM_001080392.2:c.268+2744A>G

Variant summary

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

The NM_001080392.2(DENND11):​c.268+2744A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 151,910 control chromosomes in the GnomAD database, including 30,907 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 0.63 (30907 hom., cov: 30)
• Consequence: DENND11 NM_001080392.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 8 publications found

Genes affected

DENND11 (HGNC:29472): (DENN domain containing 11) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of catalytic activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080392.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DENND11	NM_001080392.2	MANE Select	c.268+2744A>G		intron	N/A	NP_001073861.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DENND11	ENST00000536163.6	TSL:1 MANE Select	c.268+2744A>G		intron	N/A	ENSP00000445768.1
	DENND11	ENST00000482493.1	TSL:5	c.-6+2414A>G		intron	N/A	ENSP00000418236.1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95447 AN: 151792 Hom.: 30887 Cov.: 30

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.629 AC: 95519 AN: 151910 Hom.: 30907 Cov.: 30 AF XY: 0.629 AC XY: 46712 AN XY: 74254

African (AFR) AF: 0.791 AC: 32785 AN: 41436

American (AMR) AF: 0.532 AC: 8125 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2080 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2413 AN: 5144

South Asian (SAS) AF: 0.717 AC: 3436 AN: 4794

European-Finnish (FIN) AF: 0.595 AC: 6282 AN: 10552

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38406 AN: 67934

Other (OTH) AF: 0.590 AC: 1249 AN: 2116

Alfa AF: 0.584 Hom.: 71482

Bravo AF: 0.625

Asia WGS AF: 0.605 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.57
PhyloP100		-0.28
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: rs13231650; hg19: chr7-141398942;