3-32080210-G-C

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 0.674 in 152,054 control chromosomes in the GnomAD database, including 37,175 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 0.67 (37175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102447 AN: 151936 Hom.: 37172 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.674 AC: 102471 AN: 152054 Hom.: 37175 Cov.: 32 AF XY: 0.680 AC XY: 50536 AN XY: 74338

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.662

Alfa AF: 0.655 Hom.: 2313

Bravo AF: 0.650

Asia WGS AF: 0.681 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.4
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9862154; hg19: chr3-32121702;