chr8-54905169-A-C

Variant names:

• chr8-54905169-A-C
• rs1391466

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 0.805 in 152,136 control chromosomes in the GnomAD database, including 49,630 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 0.80 (49630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 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: 0.805 AC: 122306 AN: 152018 Hom.: 49572 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.805 AC: 122416 AN: 152136 Hom.: 49630 Cov.: 32 AF XY: 0.806 AC XY: 59924 AN XY: 74358

African (AFR) AF: 0.905 AC: 37590 AN: 41538

American (AMR) AF: 0.766 AC: 11691 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2440 AN: 3470

East Asian (EAS) AF: 0.823 AC: 4260 AN: 5174

South Asian (SAS) AF: 0.881 AC: 4244 AN: 4818

European-Finnish (FIN) AF: 0.780 AC: 8238 AN: 10566

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51355 AN: 67988

Other (OTH) AF: 0.768 AC: 1623 AN: 2114

Alfa AF: 0.766 Hom.: 15370

Bravo AF: 0.806

Asia WGS AF: 0.828 AC: 2873 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	10
DANN	Benign	0.91
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1391466; hg19: chr8-55817729;