rs16891530

Variant names:

• chr8-42676422-G-A
• rs16891530

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 0.0538 in 152,216 control chromosomes in the GnomAD database, including 276 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 0.054 (276 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.082 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: 0.0538 AC: 8179 AN: 152098 Hom.: 274 Cov.: 31

Gnomad AFR AF: 0.0839

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0889

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0533

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

GnomAD4 genome AF: 0.0538 AC: 8196 AN: 152216 Hom.: 276 Cov.: 31 AF XY: 0.0541 AC XY: 4029 AN XY: 74418

African (AFR) AF: 0.0843 AC: 3502 AN: 41536

American (AMR) AF: 0.0354 AC: 541 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0888 AC: 429 AN: 4832

European-Finnish (FIN) AF: 0.0499 AC: 529 AN: 10596

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0386 AC: 2627 AN: 68010

Other (OTH) AF: 0.0522 AC: 110 AN: 2106

Alfa AF: 0.0447 Hom.: 485

Bravo AF: 0.0535

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.72
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs16891530; hg19: chr8-42531565;