rs33751

Variant names:

• chr3-45226624-T-C
• rs33751

Your query was ambiguous. Multiple possible variants found:

• chr3-45226624-T-C
• chr3-45226624-T-G

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 0.756 in 152,104 control chromosomes in the GnomAD database, including 46,528 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 0.76 (46528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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: 0.757 AC: 114997 AN: 151990 Hom.: 46509 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.756 AC: 115057 AN: 152104 Hom.: 46528 Cov.: 32 AF XY: 0.765 AC XY: 56875 AN XY: 74354

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.793

Alfa AF: 0.753 Hom.: 7533

Bravo AF: 0.733

Asia WGS AF: 0.909 AC: 3163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs33751; hg19: chr3-45268116;