chr9-115228913-G-A

Position:

• chr9-115228913-G-A

Variant summary

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

The ENST00000374016.5(DELEC1):​n.52-4263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,126 control chromosomes in the GnomAD database, including 413 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 0.067 (413 hom., cov: 32)
• Consequence: DELEC1 ENST00000374016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

DELEC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DELEC1	NR_163556.1	n.52-4263G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000374016.5	n.52-4263G>A		intron_variant		1
DELEC1	ENST00000484171.2	n.147-4263G>A		intron_variant		1
DELEC1	ENST00000647970.1	n.139-4263G>A		intron_variant
DELEC1	ENST00000649121.1	n.659-4263G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10239 AN: 152008 Hom.: 412 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.0673 AC: 10238 AN: 152126 Hom.: 413 Cov.: 32 AF XY: 0.0656 AC XY: 4879 AN XY: 74378

Gnomad4 AFR AF: 0.0181

Gnomad4 AMR AF: 0.0817

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0512

Gnomad4 FIN AF: 0.0666

Gnomad4 NFE AF: 0.0979

Gnomad4 OTH AF: 0.0894

Alfa AF: 0.0870 Hom.: 346

Bravo AF: 0.0664

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.40

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: rs955387; hg19: chr9-117991192;