chr8-42675289-A-G

Variant names:

• chr8-42675289-A-G
• rs16891521

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 0.0536 in 152,276 control chromosomes in the GnomAD database, including 272 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 (272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.759
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0818 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: 0.0536 AC: 8150 AN: 152158 Hom.: 270 Cov.: 32

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0889

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0530

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

GnomAD4 genome AF: 0.0536 AC: 8166 AN: 152276 Hom.: 272 Cov.: 32 AF XY: 0.0540 AC XY: 4022 AN XY: 74450

African (AFR) AF: 0.0837 AC: 3478 AN: 41574

American (AMR) AF: 0.0353 AC: 539 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4822

European-Finnish (FIN) AF: 0.0499 AC: 529 AN: 10600

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

European-Non Finnish (NFE) AF: 0.0386 AC: 2624 AN: 68024

Other (OTH) AF: 0.0520 AC: 110 AN: 2116

Alfa AF: 0.0445 Hom.: 59

Bravo AF: 0.0533

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	-0.94
CADD	Benign	6.4
DANN	Benign	0.38
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs16891521; hg19: chr8-42530432;