rs12292915

Variant names:

• chr11-18016571-C-A
• rs12292915
• ENST00000525523.1:n.285+4444G>T

Variant summary

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

The ENST00000525523.1(ENSG00000255448):​n.285+4444G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,954 control chromosomes in the GnomAD database, including 19,039 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 0.48 (19039 hom., cov: 32)
• Consequence: ENSG00000255448 ENST00000525523.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

ENSG00000255448 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 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
ENSG00000255448	ENST00000525523.1	n.285+4444G>T		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73463 AN: 151836 Hom.: 19037 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.484 AC: 73493 AN: 151954 Hom.: 19039 Cov.: 32 AF XY: 0.482 AC XY: 35800 AN XY: 74252

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.507

Alfa AF: 0.552 Hom.: 23298

Bravo AF: 0.474

Asia WGS AF: 0.516 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.22
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12292915; hg19: chr11-18038118;