chr12-21128833-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000257062 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593147.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257062	ENST00000593147.5	TSL:5	n.*115-2290C>T		intron	N/A	ENSP00000467209.1
	ENSG00000257062	ENST00000543498.5	TSL:4	n.279-12681C>T		intron	N/A	ENSP00000454306.1
	ENSG00000257062	ENST00000585342.5	TSL:4	n.*101-2290C>T		intron	N/A	ENSP00000467594.1

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

African (AFR) AF: 0.736 AC: 30421 AN: 41322

American (AMR) AF: 0.933 AC: 14227 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3273 AN: 3468

East Asian (EAS) AF: 0.851 AC: 4375 AN: 5138

South Asian (SAS) AF: 0.955 AC: 4586 AN: 4802

European-Finnish (FIN) AF: 0.910 AC: 9617 AN: 10570

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 63917 AN: 67938

Other (OTH) AF: 0.891 AC: 1876 AN: 2106

Alfa AF: 0.923 Hom.: 272894

Bravo AF: 0.875

Asia WGS AF: 0.898 AC: 3124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.26
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs852550; hg19: chr12-21281767;