rs1391466

chr8-54905169-A-C

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 0.805 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.768

Alfa AF: 0.764 Hom.: 11894

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1391466; hg19: chr8-55817729;