rs10261374

Variant names:

• chr7-141698788-A-T
• rs10261374
• NM_001080392.2:c.268+3098T>A

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+3098T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,004 control chromosomes in the GnomAD database, including 32,547 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 0.64 (32547 hom., cov: 32)
• Consequence: DENND11 NM_001080392.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 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+3098T>A		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+3098T>A		intron	N/A	ENSP00000445768.1
	DENND11	ENST00000482493.1	TSL:5	c.-6+2768T>A		intron	N/A	ENSP00000418236.1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97613 AN: 151886 Hom.: 32522 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.643 AC: 97692 AN: 152004 Hom.: 32547 Cov.: 32 AF XY: 0.643 AC XY: 47739 AN XY: 74266

African (AFR) AF: 0.837 AC: 34755 AN: 41502

American (AMR) AF: 0.545 AC: 8309 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2097 AN: 3472

East Asian (EAS) AF: 0.472 AC: 2436 AN: 5160

South Asian (SAS) AF: 0.704 AC: 3387 AN: 4814

European-Finnish (FIN) AF: 0.594 AC: 6256 AN: 10534

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38440 AN: 67954

Other (OTH) AF: 0.602 AC: 1268 AN: 2106

Alfa AF: 0.615 Hom.: 3676

Bravo AF: 0.642

Asia WGS AF: 0.606 AC: 2109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.33
PhyloP100		-0.51
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: rs10261374; hg19: chr7-141398588;