rs8046880

Variant names:

• chr16-61001328-A-G
• rs8046880

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 0.275 in 151,940 control chromosomes in the GnomAD database, including 7,674 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 0.27 (7674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 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: 0.275 AC: 41726 AN: 151824 Hom.: 7668 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.275 AC: 41770 AN: 151940 Hom.: 7674 Cov.: 32 AF XY: 0.279 AC XY: 20745 AN XY: 74244

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.257

Alfa AF: 0.222 Hom.: 574

Bravo AF: 0.308

Asia WGS AF: 0.318 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.018
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8046880; hg19: chr16-61035232;