16-12620537-A-C

Variant names:

• chr16-12620537-A-C
• rs4780469

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 0.549 in 151,972 control chromosomes in the GnomAD database, including 23,486 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 0.55 (23486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 7 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 = 0.638 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83463 AN: 151854 Hom.: 23480 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.549 AC: 83492 AN: 151972 Hom.: 23486 Cov.: 32 AF XY: 0.551 AC XY: 40948 AN XY: 74268

African (AFR) AF: 0.448 AC: 18552 AN: 41430

American (AMR) AF: 0.649 AC: 9911 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1886 AN: 3466

East Asian (EAS) AF: 0.424 AC: 2197 AN: 5178

South Asian (SAS) AF: 0.472 AC: 2277 AN: 4824

European-Finnish (FIN) AF: 0.625 AC: 6586 AN: 10540

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40102 AN: 67950

Other (OTH) AF: 0.560 AC: 1180 AN: 2106

Alfa AF: 0.578 Hom.: 44615

Bravo AF: 0.551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.33
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs4780469; hg19: chr16-12714394;