rs9784453

Variant names:

• chr4-157469067-G-A
• rs9784453

Your query was ambiguous. Multiple possible variants found:

• 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;