rs9290705

Positions:

• chr3-180456679-T-C

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 0.091 in 152,150 control chromosomes in the GnomAD database, including 687 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 0.091 (687 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.180456679T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02053	ENST00000654328.1	n.265-18760T>C		intron_variant
LINC02053	ENST00000668671.1	n.283-2964T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13846 AN: 152032 Hom.: 686 Cov.: 32

Gnomad AFR AF: 0.0706

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.0912

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

GnomAD4 genome AF: 0.0910 AC: 13850 AN: 152150 Hom.: 687 Cov.: 32 AF XY: 0.0927 AC XY: 6891 AN XY: 74372

Gnomad4 AFR AF: 0.0704

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0792

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0981 Hom.: 1025

Bravo AF: 0.0898

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.052
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9290705; hg19: chr3-180174467;