rs16904354

Variant names:

• chr8-130777374-G-A
• rs16904354

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.186 AC: 7735 AN: 41512

American (AMR) AF: 0.0519 AC: 794 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.0118 AC: 61 AN: 5184

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4822

European-Finnish (FIN) AF: 0.0118 AC: 125 AN: 10600

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0493 AC: 3355 AN: 68024

Other (OTH) AF: 0.0870 AC: 184 AN: 2114

Alfa AF: 0.0676 Hom.: 828

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
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs16904354; hg19: chr8-131789620;