8-42673524-G-A

Position:

• chr8-42673524-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 0.692 in 152,034 control chromosomes in the GnomAD database, including 39,193 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 0.69 (39193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -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 = 0.812 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: 0.692 AC: 105093 AN: 151914 Hom.: 39181 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.692 AC: 105144 AN: 152034 Hom.: 39193 Cov.: 32 AF XY: 0.697 AC XY: 51783 AN XY: 74302

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.723

Alfa AF: 0.662 Hom.: 2140

Bravo AF: 0.672

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5005909; hg19: chr8-42528667;