16-57356267-G-C

Variant names:

• chr16-57356267-G-C
• rs76295899

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 0.028 in 152,236 control chromosomes in the GnomAD database, including 167 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 0.028 (167 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 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: 0.0280 AC: 4265 AN: 152120 Hom.: 169 Cov.: 31

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0139

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0280 AC: 4258 AN: 152236 Hom.: 167 Cov.: 31 AF XY: 0.0299 AC XY: 2224 AN XY: 74420

African (AFR) AF: 0.0195 AC: 810 AN: 41544

American (AMR) AF: 0.0501 AC: 766 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00778 AC: 27 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1146 AN: 5170

South Asian (SAS) AF: 0.0206 AC: 99 AN: 4810

European-Finnish (FIN) AF: 0.0350 AC: 371 AN: 10606

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0139 AC: 947 AN: 68028

Other (OTH) AF: 0.0331 AC: 70 AN: 2114

Alfa AF: 0.0184 Hom.: 7

Bravo AF: 0.0318

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs76295899; hg19: chr16-57390179;