3-32900360-G-T

Position:

• chr3-32900360-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 0.623 in 151,978 control chromosomes in the GnomAD database, including 29,959 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 0.62 (29959 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 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: 0.623 AC: 94577 AN: 151860 Hom.: 29942 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.623 AC: 94638 AN: 151978 Hom.: 29959 Cov.: 31 AF XY: 0.625 AC XY: 46440 AN XY: 74258

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.643

Alfa AF: 0.642 Hom.: 12878

Bravo AF: 0.621

Asia WGS AF: 0.740 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7648704; hg19: chr3-32941852;