3-44233784-C-T

Variant names:

• chr3-44233784-C-T
• rs967285

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 0.473 in 152,002 control chromosomes in the GnomAD database, including 17,888 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 0.47 (17888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71893 AN: 151884 Hom.: 17872 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.473 AC: 71951 AN: 152002 Hom.: 17888 Cov.: 32 AF XY: 0.481 AC XY: 35762 AN XY: 74276

African (AFR) AF: 0.365 AC: 15137 AN: 41418

American (AMR) AF: 0.543 AC: 8289 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3472

East Asian (EAS) AF: 0.805 AC: 4169 AN: 5180

South Asian (SAS) AF: 0.704 AC: 3389 AN: 4814

European-Finnish (FIN) AF: 0.508 AC: 5364 AN: 10550

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32180 AN: 67978

Other (OTH) AF: 0.466 AC: 986 AN: 2114

Alfa AF: 0.473 Hom.: 2916

Bravo AF: 0.471

Asia WGS AF: 0.725 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.61
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs967285; hg19: chr3-44275276;