rs13396952

Variant names:

• chr2-164880547-G-A
• rs13396952
• ENST00000414885.2:n.638+31145G>A

Variant summary

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

The ENST00000662281.1(ENSG00000236283):​n.561+31145G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0683 in 152,110 control chromosomes in the GnomAD database, including 1,092 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 0.068 (1092 hom., cov: 33)
• Consequence: ENSG00000236283 ENST00000662281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 3 publications found

Genes affected

ENSG00000236283 (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 (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662281.1. 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
	ENSG00000236283	ENST00000414885.2	TSL:5	n.638+31145G>A		intron	N/A
	ENSG00000236283	ENST00000638199.1	TSL:5	n.712+31145G>A		intron	N/A
	ENSG00000236283	ENST00000662281.1		n.561+31145G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10360 AN: 151992 Hom.: 1090 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00168

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0683 AC: 10384 AN: 152110 Hom.: 1092 Cov.: 33 AF XY: 0.0660 AC XY: 4908 AN XY: 74378

African (AFR) AF: 0.227 AC: 9425 AN: 41446

American (AMR) AF: 0.0351 AC: 536 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3470

East Asian (EAS) AF: 0.0160 AC: 83 AN: 5188

South Asian (SAS) AF: 0.0174 AC: 84 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10582

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00168 AC: 114 AN: 67998

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0666 Hom.: 491

Bravo AF: 0.0779

Asia WGS AF: 0.0310 AC: 111 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	2.6
DANN	Benign	0.51
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs13396952; hg19: chr2-165737057;