rs8054124

chr16-86400947-T-C

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 0.232 in 152,108 control chromosomes in the GnomAD database, including 4,115 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 0.23 (4115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35268 AN: 151990 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.232 AC: 35303 AN: 152108 Hom.: 4115 Cov.: 32 AF XY: 0.229 AC XY: 16997 AN XY: 74368

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.254

Alfa AF: 0.237 Hom.: 2073

Bravo AF: 0.231

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.6
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8054124; hg19: chr16-86434553;