rs16846880

Variant names:

• chr4-71728848-C-G
• rs16846880

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0302

Gnomad4 EAS AF: 0.00908

Gnomad4 SAS AF: 0.0234

Gnomad4 FIN AF: 0.0449

Gnomad4 NFE AF: 0.0752

Gnomad4 OTH AF: 0.0795

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16846880; hg19: chr4-72594565;