12-114142716-T-C

Variant names:

• chr12-114142716-T-C
• rs1920583
• ENST00000552413.2:n.1108-19512T>C

Variant summary

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

The ENST00000552413.2(ENSG00000257997):​n.1108-19512T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 152,176 control chromosomes in the GnomAD database, including 827 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 0.097 (827 hom., cov: 32)
• Consequence: ENSG00000257997 ENST00000552413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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.1108-19512T>C		intron_variant	Intron 2 of 4	4
ENSG00000257997	ENST00000777255.1	n.457-52377T>C		intron_variant	Intron 3 of 3
ENSG00000257997	ENST00000777256.1	n.449-36044T>C		intron_variant	Intron 3 of 4
ENSG00000257997	ENST00000777257.1	n.1068-36044T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14779 AN: 152058 Hom.: 828 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0745

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.0972 AC: 14793 AN: 152176 Hom.: 827 Cov.: 32 AF XY: 0.0962 AC XY: 7159 AN XY: 74400

African (AFR) AF: 0.152 AC: 6296 AN: 41502

American (AMR) AF: 0.0830 AC: 1269 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3470

East Asian (EAS) AF: 0.0746 AC: 386 AN: 5172

South Asian (SAS) AF: 0.150 AC: 722 AN: 4822

European-Finnish (FIN) AF: 0.0607 AC: 644 AN: 10608

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0720 AC: 4897 AN: 68008

Other (OTH) AF: 0.0877 AC: 185 AN: 2110

Alfa AF: 0.0895 Hom.: 145

Bravo AF: 0.100

Asia WGS AF: 0.117 AC: 404 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.82
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1920583; hg19: chr12-114580521;