chr16-77676827-C-T

Variant names:

• chr16-77676827-C-T
• rs8051539

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 0.195 in 152,112 control chromosomes in the GnomAD database, including 3,240 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 0.20 (3240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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: 0.195 AC: 29634 AN: 151994 Hom.: 3235 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.195 AC: 29665 AN: 152112 Hom.: 3240 Cov.: 32 AF XY: 0.200 AC XY: 14862 AN XY: 74362

African (AFR) AF: 0.149 AC: 6172 AN: 41508

American (AMR) AF: 0.188 AC: 2870 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3472

East Asian (EAS) AF: 0.493 AC: 2551 AN: 5170

South Asian (SAS) AF: 0.292 AC: 1406 AN: 4820

European-Finnish (FIN) AF: 0.247 AC: 2609 AN: 10580

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12714 AN: 67980

Other (OTH) AF: 0.197 AC: 414 AN: 2104

Alfa AF: 0.195 Hom.: 13154

Bravo AF: 0.191

Asia WGS AF: 0.406 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs8051539; hg19: chr16-77710724;