rs12555345

Variant names:

• chr9-27630564-T-C
• rs12555345
• ENST00000827310.1:n.697-44178A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000827310.1(ENSG00000307594):​n.697-44178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,164 control chromosomes in the GnomAD database, including 7,660 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 0.29 (7660 hom., cov: 32)
• Consequence: ENSG00000307594 ENST00000827310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 5 publications found

Genes affected

ENSG00000307594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 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
ENSG00000307594	ENST00000827310.1	n.697-44178A>G		intron_variant	Intron 3 of 3
ENSG00000307594	ENST00000827311.1	n.389-44178A>G		intron_variant	Intron 1 of 1
ENSG00000307594	ENST00000827312.1	n.741-44178A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43639 AN: 152044 Hom.: 7654 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.287 AC: 43662 AN: 152164 Hom.: 7660 Cov.: 32 AF XY: 0.289 AC XY: 21489 AN XY: 74392

African (AFR) AF: 0.0881 AC: 3663 AN: 41560

American (AMR) AF: 0.353 AC: 5385 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1632 AN: 3466

East Asian (EAS) AF: 0.155 AC: 806 AN: 5184

South Asian (SAS) AF: 0.359 AC: 1732 AN: 4822

European-Finnish (FIN) AF: 0.348 AC: 3675 AN: 10574

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25505 AN: 67964

Other (OTH) AF: 0.319 AC: 675 AN: 2116

Alfa AF: 0.340 Hom.: 22955

Bravo AF: 0.278

Asia WGS AF: 0.226 AC: 788 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	3.0
DANN	Benign	0.68
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs12555345; hg19: chr9-27630562;