16-69525793-C-T

Variant names:

• chr16-69525793-C-T
• rs4783720

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 0.895 in 152,262 control chromosomes in the GnomAD database, including 61,248 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 0.90 (61248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.957 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: 0.895 AC: 136230 AN: 152144 Hom.: 61198 Cov.: 32

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.895 AC: 136337 AN: 152262 Hom.: 61248 Cov.: 32 AF XY: 0.897 AC XY: 66771 AN XY: 74442

African (AFR) AF: 0.965 AC: 40128 AN: 41566

American (AMR) AF: 0.875 AC: 13385 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3171 AN: 3472

East Asian (EAS) AF: 0.941 AC: 4884 AN: 5188

South Asian (SAS) AF: 0.872 AC: 4201 AN: 4820

European-Finnish (FIN) AF: 0.868 AC: 9189 AN: 10586

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58482 AN: 68020

Other (OTH) AF: 0.892 AC: 1885 AN: 2114

Alfa AF: 0.875 Hom.: 153031

Bravo AF: 0.897

Asia WGS AF: 0.910 AC: 3165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.60
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs4783720; hg19: chr16-69559696;