3-105292046-A-G

Variant names:

• chr3-105292046-A-G
• rs9810233

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 0.26 in 151,882 control chromosomes in the GnomAD database, including 5,842 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 0.26 (5842 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 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: 0.260 AC: 39453 AN: 151764 Hom.: 5839 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.260 AC: 39459 AN: 151882 Hom.: 5842 Cov.: 32 AF XY: 0.268 AC XY: 19902 AN XY: 74242

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.237

Alfa AF: 0.286 Hom.: 7410

Bravo AF: 0.252

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9810233; hg19: chr3-105010890;