12-21126908-A-G

Variant names:

• chr12-21126908-A-G
• rs704166
• ENST00000593147.5:n.*114+651A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000593147.5(ENSG00000257062):​n.*114+651A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 151,972 control chromosomes in the GnomAD database, including 61,907 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 0.90 (61907 hom., cov: 30)
• Consequence: ENSG00000257062 ENST00000593147.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.934 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.*114+651A>G		intron_variant	Intron 5 of 5	5		ENSP00000467209.1

Frequencies

GnomAD3 genomes AF: 0.901 AC: 136763 AN: 151854 Hom.: 61862 Cov.: 30

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.901 AC: 136868 AN: 151972 Hom.: 61907 Cov.: 30 AF XY: 0.901 AC XY: 66906 AN XY: 74296

African (AFR) AF: 0.809 AC: 33499 AN: 41420

American (AMR) AF: 0.939 AC: 14293 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3270 AN: 3472

East Asian (EAS) AF: 0.893 AC: 4601 AN: 5154

South Asian (SAS) AF: 0.953 AC: 4590 AN: 4816

European-Finnish (FIN) AF: 0.909 AC: 9630 AN: 10598

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63906 AN: 67976

Other (OTH) AF: 0.908 AC: 1913 AN: 2106

Alfa AF: 0.930 Hom.: 27867

Bravo AF: 0.899

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	-0.87
CADD	Benign	1.9
DANN	Benign	0.77
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs704166; hg19: chr12-21279842;