12-114129121-C-T

Variant names:

• chr12-114129121-C-T
• rs1920587
• ENST00000552413.2:n.1108-33107C>T

Variant summary

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

The ENST00000552413.2(ENSG00000257997):​n.1108-33107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0978 in 152,108 control chromosomes in the GnomAD database, including 864 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 0.098 (864 hom., cov: 33)
• Consequence: ENSG00000257997 ENST00000552413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552413.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257997	ENST00000552413.2	TSL:4	n.1108-33107C>T		intron	N/A
	ENSG00000257997	ENST00000777255.1		n.456+48671C>T		intron	N/A
	ENSG00000257997	ENST00000777256.1		n.448+48671C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0978 AC: 14868 AN: 151990 Hom.: 866 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0978 AC: 14883 AN: 152108 Hom.: 864 Cov.: 33 AF XY: 0.0967 AC XY: 7187 AN XY: 74336

African (AFR) AF: 0.160 AC: 6646 AN: 41488

American (AMR) AF: 0.0828 AC: 1265 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0613 AC: 213 AN: 3472

East Asian (EAS) AF: 0.0747 AC: 385 AN: 5152

South Asian (SAS) AF: 0.150 AC: 723 AN: 4816

European-Finnish (FIN) AF: 0.0594 AC: 629 AN: 10594

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0685 AC: 4659 AN: 67992

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.0399 Hom.: 35

Bravo AF: 0.101

Asia WGS AF: 0.120 AC: 414 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.48
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1920587; hg19: chr12-114566926;