rs8046880

Positions:

• chr16-61001328-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;