rs16846880

Variant names:

• chr4-71728848-C-G
• rs16846880

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 0.0751 in 152,232 control chromosomes in the GnomAD database, including 482 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 0.075 (482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 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: 0.0751 AC: 11430 AN: 152114 Hom.: 482 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.00906

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0449

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0751 AC: 11439 AN: 152232 Hom.: 482 Cov.: 32 AF XY: 0.0720 AC XY: 5358 AN XY: 74430

African (AFR) AF: 0.109 AC: 4507 AN: 41492

American (AMR) AF: 0.0559 AC: 855 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0302 AC: 105 AN: 3472

East Asian (EAS) AF: 0.00908 AC: 47 AN: 5176

South Asian (SAS) AF: 0.0234 AC: 113 AN: 4826

European-Finnish (FIN) AF: 0.0449 AC: 477 AN: 10622

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

European-Non Finnish (NFE) AF: 0.0752 AC: 5116 AN: 68030

Other (OTH) AF: 0.0795 AC: 168 AN: 2114

Alfa AF: 0.0706 Hom.: 48

Bravo AF: 0.0765

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.77
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs16846880; hg19: chr4-72594565;