4-157469067-G-A

Variant names:

• chr4-157469067-G-A
• rs9784453

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.364 AC: 15092 AN: 41504

American (AMR) AF: 0.296 AC: 4527 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3470

East Asian (EAS) AF: 0.187 AC: 960 AN: 5144

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4384 AN: 10572

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25762 AN: 67980

Other (OTH) AF: 0.376 AC: 796 AN: 2116

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
PhyloP100		-2.7

Splicing

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

Other links and lift over

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