rs39733

Variant names:

• chr16-3723163-T-C
• rs39733

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.942 AC: 39173 AN: 41584

American (AMR) AF: 0.803 AC: 12286 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2743 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5172 AN: 5182

South Asian (SAS) AF: 0.888 AC: 4278 AN: 4818

European-Finnish (FIN) AF: 0.714 AC: 7570 AN: 10600

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47348 AN: 68014

Other (OTH) AF: 0.800 AC: 1693 AN: 2116

Alfa AF: 0.758 Hom.: 37308

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs39733; hg19: chr16-3773164;