rs9859259

Positions:

• chr3-172505351-C-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 0.504 in 148,374 control chromosomes in the GnomAD database, including 19,994 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 0.50 (19994 hom., cov: 25)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) 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.172505351C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.504 AC: 74737 AN: 148270 Hom.: 19979 Cov.: 25

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.403

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.504 AC: 74796 AN: 148374 Hom.: 19994 Cov.: 25 AF XY: 0.499 AC XY: 35995 AN XY: 72128

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.486

Alfa AF: 0.454 Hom.: 7569

Bravo AF: 0.511

Asia WGS AF: 0.534 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
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: rs9859259; hg19: chr3-172223141;