16-85954392-A-G

Variant names:

• chr16-85954392-A-G
• rs10863202

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 0.639 in 152,208 control chromosomes in the GnomAD database, including 32,283 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 0.64 (32283 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97198 AN: 152092 Hom.: 32269 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.639 AC: 97246 AN: 152208 Hom.: 32283 Cov.: 33 AF XY: 0.648 AC XY: 48201 AN XY: 74430

African (AFR) AF: 0.460 AC: 19098 AN: 41530

American (AMR) AF: 0.686 AC: 10489 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1892 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4282 AN: 5176

South Asian (SAS) AF: 0.695 AC: 3352 AN: 4820

European-Finnish (FIN) AF: 0.834 AC: 8852 AN: 10610

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47293 AN: 67990

Other (OTH) AF: 0.618 AC: 1307 AN: 2114

Alfa AF: 0.671 Hom.: 5889

Bravo AF: 0.620

Asia WGS AF: 0.734 AC: 2551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs10863202; hg19: chr16-85987998;