16-57355742-A-G

Variant names:

• chr16-57355742-A-G
• rs223884

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 0.892 in 150,098 control chromosomes in the GnomAD database, including 60,123 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 0.89 (60123 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.945 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: 0.892 AC: 133828 AN: 149986 Hom.: 60089 Cov.: 23

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.892 AC: 133913 AN: 150098 Hom.: 60123 Cov.: 23 AF XY: 0.892 AC XY: 65354 AN XY: 73244

African (AFR) AF: 0.788 AC: 31963 AN: 40564

American (AMR) AF: 0.838 AC: 12564 AN: 15000

Ashkenazi Jewish (ASJ) AF: 0.949 AC: 3278 AN: 3454

East Asian (EAS) AF: 0.902 AC: 4544 AN: 5038

South Asian (SAS) AF: 0.904 AC: 4250 AN: 4702

European-Finnish (FIN) AF: 0.965 AC: 9979 AN: 10346

Middle Eastern (MID) AF: 0.921 AC: 269 AN: 292

European-Non Finnish (NFE) AF: 0.951 AC: 64425 AN: 67732

Other (OTH) AF: 0.900 AC: 1861 AN: 2068

Alfa AF: 0.918 Hom.: 7521

Bravo AF: 0.876

Asia WGS AF: 0.898 AC: 3124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.18
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs223884; hg19: chr16-57389654;