rs545854

Variant names:

• chr8-10002570-G-C
• rs545854
• ENST00000659604.1:n.117-11873C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659604.1(ENSG00000286622):​n.117-11873C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,132 control chromosomes in the GnomAD database, including 55,139 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 0.85 (55139 hom., cov: 30)
• Consequence: ENSG00000286622 ENST00000659604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654

Genes affected

ENSG00000286622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 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
ENSG00000286622	ENST00000659604.1	n.117-11873C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128667 AN: 152014 Hom.: 55077 Cov.: 30

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.847 AC: 128788 AN: 152132 Hom.: 55139 Cov.: 30 AF XY: 0.839 AC XY: 62368 AN XY: 74344

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.840

Alfa AF: 0.856 Hom.: 7027

Bravo AF: 0.847

Asia WGS AF: 0.671 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs545854; hg19: chr8-9860080;