chr2-183911721-C-T

Variant names:

• chr2-183911721-C-T
• rs826133
• ENST00000441026.1:n.103+7090C>T

Variant summary

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

The ENST00000441026.1(ENSG00000234172):​n.103+7090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 151,964 control chromosomes in the GnomAD database, including 50,477 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 0.81 (50477 hom., cov: 33)
• Consequence: ENSG00000234172 ENST00000441026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 0 publications found

Genes affected

ENSG00000234172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441026.1. 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
	ENSG00000234172	ENST00000441026.1	TSL:2	n.103+7090C>T		intron	N/A
	ENSG00000234172	ENST00000828168.1		n.139+7090C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123271 AN: 151846 Hom.: 50452 Cov.: 33

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.812 AC: 123348 AN: 151964 Hom.: 50477 Cov.: 33 AF XY: 0.809 AC XY: 60119 AN XY: 74272

African (AFR) AF: 0.723 AC: 29974 AN: 41452

American (AMR) AF: 0.871 AC: 13291 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2788 AN: 3470

East Asian (EAS) AF: 0.881 AC: 4565 AN: 5184

South Asian (SAS) AF: 0.841 AC: 4052 AN: 4820

European-Finnish (FIN) AF: 0.736 AC: 7777 AN: 10564

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.856 AC: 58099 AN: 67900

Other (OTH) AF: 0.818 AC: 1729 AN: 2114

Alfa AF: 0.837 Hom.: 6654

Bravo AF: 0.817

Asia WGS AF: 0.837 AC: 2896 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.13
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs826133; hg19: chr2-184776448;