16-75218429-G-A

Variant names:

• chr16-75218429-G-A
• rs8056814

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 0.159 in 152,182 control chromosomes in the GnomAD database, including 2,724 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 0.16 (2724 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24106 AN: 152064 Hom.: 2707 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0730

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0712

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.159 AC: 24146 AN: 152182 Hom.: 2724 Cov.: 33 AF XY: 0.156 AC XY: 11609 AN XY: 74404

African (AFR) AF: 0.322 AC: 13362 AN: 41492

American (AMR) AF: 0.120 AC: 1830 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0730 AC: 253 AN: 3464

East Asian (EAS) AF: 0.195 AC: 1006 AN: 5164

South Asian (SAS) AF: 0.0692 AC: 334 AN: 4828

European-Finnish (FIN) AF: 0.0839 AC: 890 AN: 10608

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0888 AC: 6040 AN: 68004

Other (OTH) AF: 0.153 AC: 323 AN: 2116

Alfa AF: 0.127 Hom.: 292

Bravo AF: 0.170

Asia WGS AF: 0.157 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.53
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs8056814; hg19: chr16-75252327;