16-57418059-C-T

Variant names:

• chr16-57418059-C-T
• rs223830

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 0.79 in 151,934 control chromosomes in the GnomAD database, including 48,230 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 (48230 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 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: 0.789 AC: 119847 AN: 151816 Hom.: 48180 Cov.: 29

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.790 AC: 119957 AN: 151934 Hom.: 48230 Cov.: 29 AF XY: 0.780 AC XY: 57911 AN XY: 74256

African (AFR) AF: 0.923 AC: 38279 AN: 41478

American (AMR) AF: 0.683 AC: 10394 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2696 AN: 3468

East Asian (EAS) AF: 0.540 AC: 2777 AN: 5138

South Asian (SAS) AF: 0.641 AC: 3088 AN: 4818

European-Finnish (FIN) AF: 0.703 AC: 7412 AN: 10538

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52723 AN: 67970

Other (OTH) AF: 0.796 AC: 1668 AN: 2096

Alfa AF: 0.784 Hom.: 5852

Bravo AF: 0.792

Asia WGS AF: 0.624 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs223830; hg19: chr16-57451971;