8-42694874-A-G

Variant names:

• chr8-42694874-A-G
• rs13280301

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 0.769 in 152,206 control chromosomes in the GnomAD database, including 45,843 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 0.77 (45843 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 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: 0.769 AC: 116981 AN: 152088 Hom.: 45813 Cov.: 33

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.769 AC: 117069 AN: 152206 Hom.: 45843 Cov.: 33 AF XY: 0.773 AC XY: 57495 AN XY: 74426

African (AFR) AF: 0.613 AC: 25453 AN: 41490

American (AMR) AF: 0.780 AC: 11918 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2847 AN: 3472

East Asian (EAS) AF: 0.807 AC: 4190 AN: 5190

South Asian (SAS) AF: 0.799 AC: 3859 AN: 4832

European-Finnish (FIN) AF: 0.846 AC: 8970 AN: 10608

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57139 AN: 68016

Other (OTH) AF: 0.772 AC: 1628 AN: 2108

Alfa AF: 0.720 Hom.: 3173

Bravo AF: 0.755

Asia WGS AF: 0.765 AC: 2661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.89
DANN	Benign	0.61
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs13280301; hg19: chr8-42550017;