ENST00000441026.1:n.103+7090C>T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000234172 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234172	ENST00000441026.1	n.103+7090C>T		intron_variant	Intron 1 of 2	2

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

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.818

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826133; hg19: chr2-184776448;