16-57356306-G-T

Variant names:

• chr16-57356306-G-T
• rs4784799

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 0.13 in 152,178 control chromosomes in the GnomAD database, including 1,553 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 0.13 (1553 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19806 AN: 152060 Hom.: 1558 Cov.: 31

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.130 AC: 19793 AN: 152178 Hom.: 1553 Cov.: 31 AF XY: 0.130 AC XY: 9654 AN XY: 74396

African (AFR) AF: 0.0498 AC: 2069 AN: 41522

American (AMR) AF: 0.124 AC: 1897 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3468

East Asian (EAS) AF: 0.278 AC: 1437 AN: 5176

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4808

European-Finnish (FIN) AF: 0.109 AC: 1157 AN: 10598

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11205 AN: 68002

Other (OTH) AF: 0.136 AC: 288 AN: 2114

Alfa AF: 0.0382 Hom.: 35

Bravo AF: 0.129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs4784799; hg19: chr16-57390218; COSMIC: COSV107265778;