rs11763011

Positions:

• chr7-73869818-A-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 0.483 in 151,802 control chromosomes in the GnomAD database, including 18,900 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 0.48 (18900 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

Genes affected

(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 = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73869818A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73307 AN: 151686 Hom.: 18888 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.483 AC: 73357 AN: 151802 Hom.: 18900 Cov.: 31 AF XY: 0.481 AC XY: 35666 AN XY: 74168

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.476

Alfa AF: 0.561 Hom.: 19421

Bravo AF: 0.470

Asia WGS AF: 0.409 AC: 1427 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	1.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11763011; hg19: chr7-73284148;