3-105292046-A-G

Variant names:

• chr3-105292046-A-G
• rs9810233

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.138 AC: 5725 AN: 41474

American (AMR) AF: 0.272 AC: 4135 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2856 AN: 5156

South Asian (SAS) AF: 0.342 AC: 1646 AN: 4816

European-Finnish (FIN) AF: 0.375 AC: 3947 AN: 10520

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19152 AN: 67908

Other (OTH) AF: 0.237 AC: 502 AN: 2114

Alfa AF: 0.278 Hom.: 12343

Bravo AF: 0.252

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
DANN	Benign	0.95
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs9810233; hg19: chr3-105010890;