rs2225481

Variant names:

• chr13-89145649-A-G
• rs2225481
• ENST00000661729.2:n.386-3518T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-89145649-A-G
• chr13-89145649-A-T

Variant summary

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

The ENST00000661729.2(ENSG00000288552):​n.386-3518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,816 control chromosomes in the GnomAD database, including 35,520 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 0.67 (35520 hom., cov: 32)
• Consequence: ENSG00000288552 ENST00000661729.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 2 publications found

Genes affected

ENSG00000288552 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661729.2. 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
	ENSG00000288552	ENST00000661729.2		n.386-3518T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.672 AC: 101930 AN: 151698 Hom.: 35515 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.672 AC: 101962 AN: 151816 Hom.: 35520 Cov.: 32 AF XY: 0.670 AC XY: 49691 AN XY: 74206

African (AFR) AF: 0.478 AC: 19782 AN: 41426

American (AMR) AF: 0.802 AC: 12212 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2539 AN: 3466

East Asian (EAS) AF: 0.737 AC: 3786 AN: 5140

South Asian (SAS) AF: 0.764 AC: 3686 AN: 4824

European-Finnish (FIN) AF: 0.615 AC: 6505 AN: 10582

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 50976 AN: 67834

Other (OTH) AF: 0.712 AC: 1498 AN: 2104

Alfa AF: 0.739 Hom.: 56139

Bravo AF: 0.679

Asia WGS AF: 0.769 AC: 2674 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.3
DANN	Benign	0.64
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs2225481; hg19: chr13-89797903;