rs10858911

Variant names:

• chr12-89569364-G-A
• rs10858911
• ENST00000552778.2:n.147+8089G>A

Variant summary

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

The ENST00000552778.2(ENSG00000258302):​n.147+8089G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,768 control chromosomes in the GnomAD database, including 21,497 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 0.52 (21497 hom., cov: 31)
• Consequence: ENSG00000258302 ENST00000552778.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491

Genes affected

ENSG00000258302 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 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
ENSG00000258302	ENST00000552778.2	n.147+8089G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78789 AN: 151652 Hom.: 21459 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.520 AC: 78872 AN: 151768 Hom.: 21497 Cov.: 31 AF XY: 0.512 AC XY: 38000 AN XY: 74184

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.478

Alfa AF: 0.494 Hom.: 4749

Bravo AF: 0.522

Asia WGS AF: 0.365 AC: 1273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10858911; hg19: chr12-89963141;