16-85958099-A-C

Variant names:

• chr16-85958099-A-C
• rs11642873

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 0.146 in 151,832 control chromosomes in the GnomAD database, including 2,117 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 0.15 (2117 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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: 0.146 AC: 22180 AN: 151714 Hom.: 2117 Cov.: 31

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0823

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.146 AC: 22182 AN: 151832 Hom.: 2117 Cov.: 31 AF XY: 0.147 AC XY: 10945 AN XY: 74204

African (AFR) AF: 0.0547 AC: 2264 AN: 41386

American (AMR) AF: 0.0820 AC: 1252 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3470

East Asian (EAS) AF: 0.0925 AC: 477 AN: 5158

South Asian (SAS) AF: 0.0933 AC: 448 AN: 4802

European-Finnish (FIN) AF: 0.294 AC: 3089 AN: 10524

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14094 AN: 67916

Other (OTH) AF: 0.105 AC: 221 AN: 2106

Alfa AF: 0.178 Hom.: 11872

Bravo AF: 0.123

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.058
DANN	Benign	0.48
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs11642873; hg19: chr16-85991705;