rs2335306

Positions:

• chr16-32446347-T-A
• chr16-32446347-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.0092 (1 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00 AC: 999 AN: 108964 Hom.: 1 Cov.: 30 FAILED QC

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.00147

Gnomad AMR AF: 0.00889

Gnomad ASJ AF: 0.00510

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.0115

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0156

Gnomad NFE AF: 0.00627

Gnomad OTH AF: 0.0104

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00917 AC: 1000 AN: 109062 Hom.: 1 Cov.: 30 AF XY: 0.00958 AC XY: 513 AN XY: 53522

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.00897

Gnomad4 ASJ AF: 0.00510

Gnomad4 EAS AF: 0.0172

Gnomad4 SAS AF: 0.0118

Gnomad4 FIN AF: 0.0162

Gnomad4 NFE AF: 0.00627

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.109 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2335306; hg19: chr16-32457668;