ENST00000452364.1:n.1152-1851T>C

Variant names:

• chr2-100997860-A-G
• rs1374324
• ENST00000452364.1:n.1152-1851T>C

Variant summary

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

The ENST00000452364.1(ENSG00000223947):​n.1152-1851T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,024 control chromosomes in the GnomAD database, including 28,707 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 0.61 (28707 hom., cov: 32)
• Consequence: ENSG00000223947 ENST00000452364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 8 publications found

Genes affected

ENSG00000223947 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452364.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223947	ENST00000452364.1	TSL:1	n.1152-1851T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92185 AN: 151906 Hom.: 28699 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.607 AC: 92224 AN: 152024 Hom.: 28707 Cov.: 32 AF XY: 0.603 AC XY: 44779 AN XY: 74314

African (AFR) AF: 0.503 AC: 20829 AN: 41448

American (AMR) AF: 0.579 AC: 8844 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2571 AN: 3472

East Asian (EAS) AF: 0.393 AC: 2032 AN: 5170

South Asian (SAS) AF: 0.595 AC: 2866 AN: 4814

European-Finnish (FIN) AF: 0.595 AC: 6284 AN: 10554

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46617 AN: 67970

Other (OTH) AF: 0.634 AC: 1338 AN: 2112

Alfa AF: 0.621 Hom.: 4880

Bravo AF: 0.599

Asia WGS AF: 0.482 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.24
DANN	Benign	0.53
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1374324; hg19: chr2-101614322;