ENST00000552413.2:n.1108-35889C>G

Variant names:

• chr12-114126339-C-G
• rs10492331
• ENST00000552413.2:n.1108-35889C>G

Variant summary

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

The ENST00000552413.2(ENSG00000257997):​n.1108-35889C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,204 control chromosomes in the GnomAD database, including 1,032 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 0.10 (1032 hom., cov: 32)
• Consequence: ENSG00000257997 ENST00000552413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 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

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
	ENSG00000257997	ENST00000552413.2	TSL:4	n.1108-35889C>G		intron	N/A
	ENSG00000257997	ENST00000777255.1		n.456+45889C>G		intron	N/A
	ENSG00000257997	ENST00000777256.1		n.448+45889C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15415 AN: 152086 Hom.: 1035 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.101 AC: 15415 AN: 152204 Hom.: 1032 Cov.: 32 AF XY: 0.103 AC XY: 7632 AN XY: 74400

African (AFR) AF: 0.0267 AC: 1107 AN: 41536

American (AMR) AF: 0.0924 AC: 1413 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3472

East Asian (EAS) AF: 0.252 AC: 1303 AN: 5178

South Asian (SAS) AF: 0.107 AC: 514 AN: 4822

European-Finnish (FIN) AF: 0.128 AC: 1357 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9023 AN: 67994

Other (OTH) AF: 0.0956 AC: 202 AN: 2114

Alfa AF: 0.0560 Hom.: 61

Bravo AF: 0.0957

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.70
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10492331; hg19: chr12-114564144;