12-21128955-T-G

Variant names:

• chr12-21128955-T-G
• rs852549
• ENST00000593147.5:n.*115-2168T>G

Variant summary

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

The ENST00000593147.5(ENSG00000257062):​n.*115-2168T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 151,922 control chromosomes in the GnomAD database, including 59,939 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 (59939 hom., cov: 29)
• Consequence: ENSG00000257062 ENST00000593147.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

Genes affected

ENSG00000257062 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.945 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.*115-2168T>G		intron_variant	Intron 5 of 5	5		ENSP00000467209.1

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134177 AN: 151804 Hom.: 59894 Cov.: 29

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.884 AC: 134280 AN: 151922 Hom.: 59939 Cov.: 29 AF XY: 0.884 AC XY: 65684 AN XY: 74262

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.943

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.899

Alfa AF: 0.933 Hom.: 86935

Bravo AF: 0.880

Asia WGS AF: 0.928 AC: 3225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs852549; hg19: chr12-21281889;