12-52521388-G-T

Variant names:

• chr12-52521388-G-T
• rs89962
• ENST00000794060.1:n.550+4723G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000794060.1(ENSG00000303382):​n.550+4723G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,238 control chromosomes in the GnomAD database, including 8,508 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 0.29 (8508 hom., cov: 33)
• Consequence: ENSG00000303382 ENST00000794060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 10 publications found

Genes affected

ENSG00000303382 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794060.1. 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
	ENSG00000303382	ENST00000794060.1		n.550+4723G>T		intron	N/A
	ENSG00000303382	ENST00000794061.1		n.381-16780G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44179 AN: 152120 Hom.: 8508 Cov.: 33

Gnomad AFR AF: 0.0738

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.00924

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.290 AC: 44174 AN: 152238 Hom.: 8508 Cov.: 33 AF XY: 0.282 AC XY: 21011 AN XY: 74422

African (AFR) AF: 0.0735 AC: 3055 AN: 41560

American (AMR) AF: 0.260 AC: 3979 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3472

East Asian (EAS) AF: 0.00927 AC: 48 AN: 5180

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4822

European-Finnish (FIN) AF: 0.358 AC: 3799 AN: 10600

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29736 AN: 67990

Other (OTH) AF: 0.308 AC: 651 AN: 2112

Alfa AF: 0.392 Hom.: 39239

Bravo AF: 0.269

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	21
DANN	Benign	0.90
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs89962; hg19: chr12-52915172;