rs9870146

Positions:

• chr3-117437408-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 0.542 in 152,054 control chromosomes in the GnomAD database, including 26,693 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 0.54 (26693 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117437408C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82448 AN: 151936 Hom.: 26702 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.542 AC: 82437 AN: 152054 Hom.: 26693 Cov.: 33 AF XY: 0.538 AC XY: 40028 AN XY: 74336

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.562

Alfa AF: 0.671 Hom.: 22954

Bravo AF: 0.519

Asia WGS AF: 0.446 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9870146; hg19: chr3-117156255;