ENST00000652339.1:n.510-2820C>T

Variant names:

• chr12-53893377-C-T
• rs2577864
• ENST00000652339.1:n.510-2820C>T

Variant summary

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

The ENST00000652339.1(ENSG00000286069):​n.510-2820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,100 control chromosomes in the GnomAD database, including 11,397 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 0.38 (11397 hom., cov: 32)
• Consequence: ENSG00000286069 ENST00000652339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 2 publications found

Genes affected

ENSG00000286069 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652339.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105378250	NR_189097.1		n.399-2820C>T		intron	N/A
	LOC105378250	NR_189098.1		n.591-2820C>T		intron	N/A
	LOC105378250	NR_189099.1		n.592-2820C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286069	ENST00000652339.1		n.510-2820C>T		intron	N/A
	ENSG00000286069	ENST00000654713.2		n.318-2820C>T		intron	N/A
	ENSG00000286069	ENST00000656247.1		n.345-2820C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58149 AN: 151982 Hom.: 11392 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.382 AC: 58166 AN: 152100 Hom.: 11397 Cov.: 32 AF XY: 0.375 AC XY: 27850 AN XY: 74356

African (AFR) AF: 0.414 AC: 17187 AN: 41488

American (AMR) AF: 0.277 AC: 4227 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1186 AN: 5174

South Asian (SAS) AF: 0.362 AC: 1742 AN: 4818

European-Finnish (FIN) AF: 0.320 AC: 3382 AN: 10562

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27772 AN: 67990

Other (OTH) AF: 0.352 AC: 745 AN: 2114

Alfa AF: 0.387 Hom.: 1946

Bravo AF: 0.378

Asia WGS AF: 0.296 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.49
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2577864; hg19: chr12-54287161;