rs1322060

Positions:

• chr9-114935380-C-G

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 0.489 in 152,012 control chromosomes in the GnomAD database, including 19,336 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 0.49 (19336 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.114935380C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DELEC1	ENST00000648852.1	n.198+13782C>G		intron_variant
DELEC1	ENST00000649565.1	n.226-34204C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74275 AN: 151894 Hom.: 19290 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.489 AC: 74383 AN: 152012 Hom.: 19336 Cov.: 32 AF XY: 0.488 AC XY: 36279 AN XY: 74280

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.459

Alfa AF: 0.461 Hom.: 2124

Bravo AF: 0.503

Asia WGS AF: 0.424 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.071
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322060; hg19: chr9-117697660;