9-114865289-G-T

Position:

• chr9-114865289-G-T

Variant summary

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

The variant allele was found at a frequency of 0.774 in 152,146 control chromosomes in the GnomAD database, including 46,512 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 0.77 (46512 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.114865289G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000648852.1	n.49+14273G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117643 AN: 152028 Hom.: 46442 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.774 AC: 117778 AN: 152146 Hom.: 46512 Cov.: 32 AF XY: 0.776 AC XY: 57683 AN XY: 74368

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.744

Alfa AF: 0.710 Hom.: 76385

Bravo AF: 0.782

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.045
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7866342; hg19: chr9-117627569;