chr3-44233784-C-T

Variant names:

• chr3-44233784-C-T
• rs967285

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 0.473 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.473 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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.466

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs967285; hg19: chr3-44275276;