3-44235847-C-T

Variant names:

• chr3-44235847-C-T
• rs9852733

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 0.456 in 151,858 control chromosomes in the GnomAD database, including 16,936 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 0.46 (16936 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 1 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 = 0.76 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: 0.456 AC: 69189 AN: 151742 Hom.: 16925 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.456 AC: 69232 AN: 151858 Hom.: 16936 Cov.: 31 AF XY: 0.464 AC XY: 34447 AN XY: 74184

African (AFR) AF: 0.309 AC: 12780 AN: 41390

American (AMR) AF: 0.537 AC: 8184 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3470

East Asian (EAS) AF: 0.780 AC: 4023 AN: 5156

South Asian (SAS) AF: 0.702 AC: 3378 AN: 4814

European-Finnish (FIN) AF: 0.508 AC: 5337 AN: 10516

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32133 AN: 67962

Other (OTH) AF: 0.457 AC: 962 AN: 2104

Alfa AF: 0.479 Hom.: 9193

Bravo AF: 0.450

Asia WGS AF: 0.712 AC: 2475 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	9.1
DANN	Benign	0.86
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs9852733; hg19: chr3-44277339;