rs16894980

Variant names:

• chr8-121252537-C-T
• rs16894980

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 0.0721 in 152,218 control chromosomes in the GnomAD database, including 733 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 0.072 (733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

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 (AFR) allele frequency at 95% confidence interval = 0.165 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: 0.0720 AC: 10950 AN: 152100 Hom.: 733 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0721 AC: 10972 AN: 152218 Hom.: 733 Cov.: 32 AF XY: 0.0741 AC XY: 5514 AN XY: 74428

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0961

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.0832

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0307

Gnomad4 NFE AF: 0.0134

Gnomad4 OTH AF: 0.0657

Alfa AF: 0.0285 Hom.: 253

Bravo AF: 0.0798

Asia WGS AF: 0.123 AC: 425 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	0.92
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16894980; hg19: chr8-122264777;