rs3309

Variant names:

• chr5-56796952-T-A
• rs3309

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 0.636 in 151,866 control chromosomes in the GnomAD database, including 31,693 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 0.64 (31693 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 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: 0.636 AC: 96505 AN: 151748 Hom.: 31675 Cov.: 30

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.636 AC: 96555 AN: 151866 Hom.: 31693 Cov.: 30 AF XY: 0.627 AC XY: 46503 AN XY: 74224

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.636

Alfa AF: 0.664 Hom.: 4248

Bravo AF: 0.618

Asia WGS AF: 0.390 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3309; hg19: chr5-56092779;