ENST00000552413.2:n.1108-32909A>G

Variant names:

• chr12-114129319-A-G
• rs1920586
• ENST00000552413.2:n.1108-32909A>G

Variant summary

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

The ENST00000552413.2(ENSG00000257997):​n.1108-32909A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,992 control chromosomes in the GnomAD database, including 31,978 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 0.64 (31978 hom., cov: 32)
• Consequence: ENSG00000257997 ENST00000552413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 6 publications found

Genes affected

ENSG00000257997 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 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
ENSG00000257997	ENST00000552413.2	n.1108-32909A>G		intron_variant	Intron 2 of 4	4
ENSG00000257997	ENST00000777255.1	n.456+48869A>G		intron_variant	Intron 3 of 3
ENSG00000257997	ENST00000777256.1	n.448+48869A>G		intron_variant	Intron 3 of 4
ENSG00000257997	ENST00000777257.1	n.1067+48869A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97066 AN: 151874 Hom.: 31933 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.639 AC: 97169 AN: 151992 Hom.: 31978 Cov.: 32 AF XY: 0.641 AC XY: 47657 AN XY: 74294

African (AFR) AF: 0.782 AC: 32441 AN: 41466

American (AMR) AF: 0.703 AC: 10738 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2061 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2828 AN: 5148

South Asian (SAS) AF: 0.695 AC: 3343 AN: 4812

European-Finnish (FIN) AF: 0.575 AC: 6083 AN: 10586

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37562 AN: 67930

Other (OTH) AF: 0.637 AC: 1341 AN: 2104

Alfa AF: 0.593 Hom.: 3004

Bravo AF: 0.656

Asia WGS AF: 0.637 AC: 2213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.39
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs1920586; hg19: chr12-114567124;