rs4392391

Variant names:

• chr3-44231474-G-A
• rs4392391

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 0.477 in 152,040 control chromosomes in the GnomAD database, including 18,098 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 0.48 (18098 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.477 AC: 72398 AN: 151920 Hom.: 18079 Cov.: 33

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.477 AC: 72462 AN: 152040 Hom.: 18098 Cov.: 33 AF XY: 0.484 AC XY: 36010 AN XY: 74334

African (AFR) AF: 0.376 AC: 15587 AN: 41432

American (AMR) AF: 0.543 AC: 8303 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3468

East Asian (EAS) AF: 0.804 AC: 4171 AN: 5190

South Asian (SAS) AF: 0.704 AC: 3395 AN: 4820

European-Finnish (FIN) AF: 0.510 AC: 5382 AN: 10556

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32198 AN: 67976

Other (OTH) AF: 0.471 AC: 990 AN: 2104

Alfa AF: 0.475 Hom.: 2938

Bravo AF: 0.474

Asia WGS AF: 0.726 AC: 2525 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.49
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs4392391; hg19: chr3-44272966;