rs4392391

Positions:

• chr3-44231474-G-A

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 0.477 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.471

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4392391; hg19: chr3-44272966;