rs3852724

Variant names:

• chr16-82612489-A-C
• rs3852724

Your query was ambiguous. Multiple possible variants found:

• chr16-82612489-A-C
• chr16-82612489-A-T

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 0.792 in 152,188 control chromosomes in the GnomAD database, including 48,301 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 0.79 (48301 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 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: 0.792 AC: 120492 AN: 152070 Hom.: 48255 Cov.: 33

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.792 AC: 120596 AN: 152188 Hom.: 48301 Cov.: 33 AF XY: 0.785 AC XY: 58414 AN XY: 74390

African (AFR) AF: 0.817 AC: 33942 AN: 41534

American (AMR) AF: 0.727 AC: 11125 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2581 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2187 AN: 5156

South Asian (SAS) AF: 0.742 AC: 3581 AN: 4828

European-Finnish (FIN) AF: 0.780 AC: 8254 AN: 10576

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56234 AN: 68010

Other (OTH) AF: 0.773 AC: 1630 AN: 2110

Alfa AF: 0.791 Hom.: 8721

Bravo AF: 0.787

Asia WGS AF: 0.586 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.66
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs3852724; hg19: chr16-82646094;