2-183911462-G-T

Variant names:

• chr2-183911462-G-T
• rs826134
• ENST00000441026.1:n.103+6831G>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+6831G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,026 control chromosomes in the GnomAD database, including 58,499 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 0.88 (58499 hom., cov: 31)
• Consequence: ENSG00000234172 ENST00000441026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 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+6831G>T		intron_variant	Intron 1 of 2	2
ENSG00000234172	ENST00000828168.1	n.139+6831G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133088 AN: 151908 Hom.: 58450 Cov.: 31

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.876 AC: 133196 AN: 152026 Hom.: 58499 Cov.: 31 AF XY: 0.878 AC XY: 65215 AN XY: 74300

African (AFR) AF: 0.894 AC: 37098 AN: 41498

American (AMR) AF: 0.891 AC: 13584 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2822 AN: 3468

East Asian (EAS) AF: 0.961 AC: 4970 AN: 5170

South Asian (SAS) AF: 0.896 AC: 4324 AN: 4828

European-Finnish (FIN) AF: 0.853 AC: 9016 AN: 10574

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58477 AN: 67920

Other (OTH) AF: 0.863 AC: 1823 AN: 2112

Alfa AF: 0.864 Hom.: 3085

Bravo AF: 0.879

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.76
DANN	Benign	0.74
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs826134; hg19: chr2-184776189;