rs16884060

Variant names:

• chr5-10060185-C-A
• rs16884060

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 0.175 in 152,172 control chromosomes in the GnomAD database, including 2,991 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 0.18 (2991 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 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: 0.175 AC: 26635 AN: 152054 Hom.: 2986 Cov.: 33

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.175 AC: 26654 AN: 152172 Hom.: 2991 Cov.: 33 AF XY: 0.179 AC XY: 13298 AN XY: 74384

Gnomad4 AFR AF: 0.0499

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.182

Alfa AF: 0.203 Hom.: 4528

Bravo AF: 0.162

Asia WGS AF: 0.322 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	8.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16884060; hg19: chr5-10060297;