16-57418253-A-G

Variant names:

• chr16-57418253-A-G
• rs188872

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 0.802 in 149,562 control chromosomes in the GnomAD database, including 48,823 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 0.80 (48823 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.802 AC: 119849 AN: 149448 Hom.: 48773 Cov.: 24

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.802 AC: 119959 AN: 149562 Hom.: 48823 Cov.: 24 AF XY: 0.795 AC XY: 57890 AN XY: 72824

African (AFR) AF: 0.937 AC: 38067 AN: 40634

American (AMR) AF: 0.704 AC: 10451 AN: 14838

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2688 AN: 3462

East Asian (EAS) AF: 0.622 AC: 3123 AN: 5018

South Asian (SAS) AF: 0.701 AC: 3316 AN: 4732

European-Finnish (FIN) AF: 0.721 AC: 7183 AN: 9956

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.777 AC: 52548 AN: 67658

Other (OTH) AF: 0.807 AC: 1664 AN: 2062

Alfa AF: 0.773 Hom.: 31086

Bravo AF: 0.804

Asia WGS AF: 0.703 AC: 2448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs188872; hg19: chr16-57452165;