rs3763869

Positions:

• chr11-9573280-G-A

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 0.58 in 152,168 control chromosomes in the GnomAD database, including 26,019 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 0.58 (26019 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.9573280G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88195 AN: 152050 Hom.: 25985 Cov.: 34

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.580 AC: 88285 AN: 152168 Hom.: 26019 Cov.: 34 AF XY: 0.581 AC XY: 43233 AN XY: 74418

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.530

Alfa AF: 0.607 Hom.: 24363

Bravo AF: 0.560

Asia WGS AF: 0.496 AC: 1726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763869; hg19: chr11-9594827;