rs16920160

Variant names:

• chr8-54395731-G-A
• rs16920160

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 0.0486 in 152,232 control chromosomes in the GnomAD database, including 241 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 0.049 (241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.071 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: 0.0487 AC: 7405 AN: 152114 Hom.: 240 Cov.: 32

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0773

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0486 AC: 7405 AN: 152232 Hom.: 241 Cov.: 32 AF XY: 0.0498 AC XY: 3706 AN XY: 74436

Gnomad4 AFR AF: 0.0114

Gnomad4 AMR AF: 0.0475

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0773

Gnomad4 SAS AF: 0.0301

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.0364

Alfa AF: 0.0565 Hom.: 296

Bravo AF: 0.0446

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16920160; hg19: chr8-55308291;