12-21128833-C-T

Variant names:

• chr12-21128833-C-T
• rs852550
• ENST00000593147.5:n.*115-2290C>T

Variant summary

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

The ENST00000593147.5(ENSG00000257062):​n.*115-2290C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 151,802 control chromosomes in the GnomAD database, including 59,297 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 0.88 (59297 hom., cov: 29)
• Consequence: ENSG00000257062 ENST00000593147.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

ENSG00000257062 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.935 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
ENSG00000257062	ENST00000593147.5	n.*115-2290C>T		intron_variant	Intron 5 of 5	5		ENSP00000467209.1

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133354 AN: 151684 Hom.: 59257 Cov.: 29

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.879 AC: 133451 AN: 151802 Hom.: 59297 Cov.: 29 AF XY: 0.880 AC XY: 65266 AN XY: 74190

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.891

Alfa AF: 0.934 Hom.: 134302

Bravo AF: 0.875

Asia WGS AF: 0.898 AC: 3124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs852550; hg19: chr12-21281767;