rs12555078

Variant names:

• chr9-73542784-G-A
• rs12555078
• ENST00000667966.1:n.269+5279C>T

Variant summary

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

The ENST00000667966.1(ENSG00000286840):​n.269+5279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0783 in 151,980 control chromosomes in the GnomAD database, including 532 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 0.078 (532 hom., cov: 32)
• Consequence: ENSG00000286840 ENST00000667966.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

Genes affected

ENSG00000286840 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.115 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
ENSG00000286840	ENST00000667966.1	n.269+5279C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0783 AC: 11891 AN: 151862 Hom.: 532 Cov.: 32

Gnomad AFR AF: 0.0879

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0459

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0783 AC: 11894 AN: 151980 Hom.: 532 Cov.: 32 AF XY: 0.0778 AC XY: 5782 AN XY: 74274

Gnomad4 AFR AF: 0.0878

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0459

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0482

Gnomad4 FIN AF: 0.0563

Gnomad4 NFE AF: 0.0765

Gnomad4 OTH AF: 0.0697

Alfa AF: 0.0746 Hom.: 274

Bravo AF: 0.0807

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12555078; hg19: chr9-76157700;