16-57356149-G-T

Variant names:

• chr16-57356149-G-T
• rs34569362

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 152,140 control chromosomes in the GnomAD database, including 1,556 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 (1556 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.266 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: 0.130 AC: 19803 AN: 152022 Hom.: 1561 Cov.: 31

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.213

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: 19790 AN: 152140 Hom.: 1556 Cov.: 31 AF XY: 0.130 AC XY: 9654 AN XY: 74362

African (AFR) AF: 0.0499 AC: 2073 AN: 41530

American (AMR) AF: 0.124 AC: 1895 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1434 AN: 5150

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4822

European-Finnish (FIN) AF: 0.109 AC: 1156 AN: 10588

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.165 AC: 11200 AN: 67984

Other (OTH) AF: 0.136 AC: 288 AN: 2112

Alfa AF: 0.141 Hom.: 264

Bravo AF: 0.129

Asia WGS AF: 0.212 AC: 735 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	12
DANN	Benign	0.78
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs34569362; hg19: chr16-57390061;