rs13013484

Variant names:

• chr2-27765954-G-A
• rs13013484
• ENST00000813860.1:n.244+245C>T

Variant summary

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

The ENST00000813860.1(ENSG00000305902):​n.244+245C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,100 control chromosomes in the GnomAD database, including 30,137 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 (30137 hom., cov: 33)
• Consequence: ENSG00000305902 ENST00000813860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.977
• Publications: 30 publications found

Genes affected

ENSG00000305902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813860.1. 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
	ENSG00000305902	ENST00000813860.1		n.244+245C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93426 AN: 151980 Hom.: 30143 Cov.: 33

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.614 AC: 93435 AN: 152100 Hom.: 30137 Cov.: 33 AF XY: 0.609 AC XY: 45302 AN XY: 74348

African (AFR) AF: 0.438 AC: 18168 AN: 41492

American (AMR) AF: 0.545 AC: 8325 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2496 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2136 AN: 5152

South Asian (SAS) AF: 0.665 AC: 3211 AN: 4828

European-Finnish (FIN) AF: 0.680 AC: 7197 AN: 10580

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49772 AN: 67990

Other (OTH) AF: 0.645 AC: 1362 AN: 2112

Alfa AF: 0.694 Hom.: 162263

Bravo AF: 0.591

Asia WGS AF: 0.516 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.1
DANN	Benign	0.90
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs13013484; hg19: chr2-27988821;