chr8-554401-G-A

Variant names:

• chr8-554401-G-A
• rs1703940

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 0.892 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.977 AC: 40534 AN: 41498

American (AMR) AF: 0.922 AC: 14079 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3125 AN: 3472

East Asian (EAS) AF: 0.818 AC: 4227 AN: 5170

South Asian (SAS) AF: 0.915 AC: 4399 AN: 4806

European-Finnish (FIN) AF: 0.715 AC: 7511 AN: 10500

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58680 AN: 67996

Other (OTH) AF: 0.899 AC: 1897 AN: 2110

Alfa AF: 0.880 Hom.: 107913

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1703940; hg19: chr8-504401;