rs16904354

chr8-130777374-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;