rs39733

chr16-3723163-T-C

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 0.795 in 152,288 control chromosomes in the GnomAD database, including 49,200 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 0.80 (49200 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

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: 0.795 AC: 121017 AN: 152170 Hom.: 49143 Cov.: 35

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.795 AC: 121135 AN: 152288 Hom.: 49200 Cov.: 35 AF XY: 0.799 AC XY: 59456 AN XY: 74438

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.800

Alfa AF: 0.747 Hom.: 20265

Bravo AF: 0.806

Asia WGS AF: 0.948 AC: 3295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.2
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs39733; hg19: chr16-3773164;