12-21128833-C-T

Position:

• chr12-21128833-C-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/exons	MANE	Protein	UniProt
		n.21128833C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257062	ENST00000593147.5	n.*115-2290C>T		intron_variant		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;