rs9312225

Positions:

• chr4-167850337-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.493 in 151,948 control chromosomes in the GnomAD database, including 19,738 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 0.49 (19738 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.167850337A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74767 AN: 151830 Hom.: 19724 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.493 AC: 74840 AN: 151948 Hom.: 19738 Cov.: 32 AF XY: 0.486 AC XY: 36068 AN XY: 74234

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.498

Alfa AF: 0.461 Hom.: 3382

Bravo AF: 0.504

Asia WGS AF: 0.293 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9312225; hg19: chr4-168771488;