chr16-80589365-C-T

Variant names:

• chr16-80589365-C-T
• rs1452501

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 0.0689 in 152,242 control chromosomes in the GnomAD database, including 918 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 0.069 (918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.263 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: 0.0687 AC: 10448 AN: 152124 Hom.: 906 Cov.: 32

Gnomad AFR AF: 0.0352

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0407

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0689 AC: 10486 AN: 152242 Hom.: 918 Cov.: 32 AF XY: 0.0746 AC XY: 5555 AN XY: 74446

African (AFR) AF: 0.0351 AC: 1460 AN: 41544

American (AMR) AF: 0.270 AC: 4124 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3466

East Asian (EAS) AF: 0.116 AC: 603 AN: 5180

South Asian (SAS) AF: 0.166 AC: 800 AN: 4822

European-Finnish (FIN) AF: 0.0356 AC: 378 AN: 10612

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0407 AC: 2771 AN: 68012

Other (OTH) AF: 0.0907 AC: 192 AN: 2116

Alfa AF: 0.0571 Hom.: 839

Bravo AF: 0.0874

Asia WGS AF: 0.140 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.37
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs1452501; hg19: chr16-80623262;