chr3-32800609-T-G

Position:

• chr3-32800609-T-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 0.11 in 152,006 control chromosomes in the GnomAD database, including 1,052 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 0.11 (1052 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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: 0.110 AC: 16684 AN: 151888 Hom.: 1052 Cov.: 31

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.110 AC: 16703 AN: 152006 Hom.: 1052 Cov.: 31 AF XY: 0.110 AC XY: 8157 AN XY: 74304

Gnomad4 AFR AF: 0.0684

Gnomad4 AMR AF: 0.0913

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.00329

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0889

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.109

Alfa AF: 0.135 Hom.: 1892

Bravo AF: 0.107

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9845475; hg19: chr3-32842101;