rs9784453

Positions:

• chr4-157469067-G-A
• chr4-157469067-G-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 0.361 in 152,098 control chromosomes in the GnomAD database, including 10,100 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 0.36 (10100 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.157469067G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54907 AN: 151980 Hom.: 10098 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.361 AC: 54926 AN: 152098 Hom.: 10100 Cov.: 33 AF XY: 0.362 AC XY: 26896 AN XY: 74326

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.376

Alfa AF: 0.260 Hom.: 823

Bravo AF: 0.353

Asia WGS AF: 0.277 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9784453; hg19: chr4-158390219; COSMIC: COSV67073085;