rs2183110

Variant names:

• chr13-109236219-A-C
• rs2183110
• ENST00000798327.1:n.62-234T>G

Your query was ambiguous. Multiple possible variants found:

• chr13-109236219-A-C
• chr13-109236219-A-G
• chr13-109236219-A-T

Variant summary

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

The ENST00000798327.1(ENSG00000303952):​n.62-234T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.984 in 152,258 control chromosomes in the GnomAD database, including 73,772 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 0.98 (73772 hom., cov: 31)
• Consequence: ENSG00000303952 ENST00000798327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 1 publications found

Genes affected

ENSG00000303952 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798327.1. 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
	ENSG00000303952	ENST00000798327.1		n.62-234T>G		intron	N/A
	ENSG00000303952	ENST00000798328.1		n.285-234T>G		intron	N/A
	ENSG00000303952	ENST00000798329.1		n.181-234T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.984 AC: 149744 AN: 152140 Hom.: 73726 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.994

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.989

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

GnomAD4 genome AF: 0.984 AC: 149849 AN: 152258 Hom.: 73772 Cov.: 31 AF XY: 0.985 AC XY: 73339 AN XY: 74440

African (AFR) AF: 0.945 AC: 39280 AN: 41548

American (AMR) AF: 0.994 AC: 15206 AN: 15298

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5145 AN: 5146

South Asian (SAS) AF: 1.00 AC: 4819 AN: 4820

European-Finnish (FIN) AF: 1.00 AC: 10626 AN: 10626

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68005 AN: 68030

Other (OTH) AF: 0.990 AC: 2092 AN: 2114

Alfa AF: 0.984 Hom.: 6522

Bravo AF: 0.982

Asia WGS AF: 0.996 AC: 3463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2183110;

hg19: chr13-109888567;