chr16-23001255-G-A

Variant names:

• chr16-23001255-G-A
• rs8045580

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 0.623 in 151,922 control chromosomes in the GnomAD database, including 30,944 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 0.62 (30944 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94527 AN: 151804 Hom.: 30926 Cov.: 31

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.623 AC: 94594 AN: 151922 Hom.: 30944 Cov.: 31 AF XY: 0.620 AC XY: 46028 AN XY: 74238

African (AFR) AF: 0.803 AC: 33259 AN: 41436

American (AMR) AF: 0.462 AC: 7053 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2270 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1230 AN: 5160

South Asian (SAS) AF: 0.748 AC: 3591 AN: 4802

European-Finnish (FIN) AF: 0.565 AC: 5957 AN: 10538

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39097 AN: 67938

Other (OTH) AF: 0.627 AC: 1321 AN: 2108

Alfa AF: 0.570 Hom.: 4346

Bravo AF: 0.616

Asia WGS AF: 0.499 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.075
DANN	Benign	0.41
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs8045580; hg19: chr16-23012576;