rs9757063

Positions:

• chr3-143264088-C-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 0.598 in 151,992 control chromosomes in the GnomAD database, including 27,930 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 0.60 (27930 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

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 (AMR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.143264088C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90841 AN: 151872 Hom.: 27920 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.598 AC: 90872 AN: 151992 Hom.: 27930 Cov.: 31 AF XY: 0.598 AC XY: 44393 AN XY: 74288

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.618

Alfa AF: 0.637 Hom.: 29889

Bravo AF: 0.594

Asia WGS AF: 0.605 AC: 2104 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	0.66
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9757063; hg19: chr3-142982930;