3-32080210-G-C

Variant names:

• chr3-32080210-G-C
• rs9862154

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;