3-46298321-A-G

Position:

• chr3-46298321-A-G

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 0.487 in 151,848 control chromosomes in the GnomAD database, including 18,598 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 0.49 (18598 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 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: 0.488 AC: 73981 AN: 151730 Hom.: 18593 Cov.: 30

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.487 AC: 74016 AN: 151848 Hom.: 18598 Cov.: 30 AF XY: 0.485 AC XY: 35956 AN XY: 74188

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.436

Alfa AF: 0.488 Hom.: 42050

Bravo AF: 0.472

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
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: rs9990343; hg19: chr3-46339812;