rs16904354

Variant names:

• chr8-130777374-G-A
• rs16904354

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 0.0832 in 152,236 control chromosomes in the GnomAD database, including 866 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 0.083 (866 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.697

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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: 0.0830 AC: 12630 AN: 152118 Hom.: 859 Cov.: 34

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0493

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0832 AC: 12661 AN: 152236 Hom.: 866 Cov.: 34 AF XY: 0.0795 AC XY: 5917 AN XY: 74442

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.0519

Gnomad4 ASJ AF: 0.0374

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0118

Gnomad4 NFE AF: 0.0493

Gnomad4 OTH AF: 0.0870

Alfa AF: 0.0745 Hom.: 150

Bravo AF: 0.0912

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16904354; hg19: chr8-131789620;