8-554401-G-A

Position:

• chr8-554401-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 0.892 in 152,026 control chromosomes in the GnomAD database, including 60,822 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 0.89 (60822 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135442 AN: 151908 Hom.: 60753 Cov.: 30

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.892 AC: 135570 AN: 152026 Hom.: 60822 Cov.: 30 AF XY: 0.885 AC XY: 65738 AN XY: 74262

Gnomad4 AFR AF: 0.977

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.899

Alfa AF: 0.876 Hom.: 76708

Bravo AF: 0.910

Asia WGS AF: 0.901 AC: 3108 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1703940; hg19: chr8-504401;