ENST00000412409.3:n.546-128990G>A

Variant names:

• chr2-59370093-C-T
• rs2192574
• ENST00000412409.3:n.546-128990G>A

Variant summary

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

The ENST00000412409.3(ENSG00000233891):​n.546-128990G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 151,674 control chromosomes in the GnomAD database, including 62,152 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 0.90 (62152 hom., cov: 31)
• Consequence: ENSG00000233891 ENST00000412409.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450
• Publications: 6 publications found

Genes affected

ENSG00000233891 (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 = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374754	XR_002959389.2	n.1447+17969G>A		intron_variant	Intron 1 of 3
LOC105374754	XR_940127.3	n.1617+14531G>A		intron_variant	Intron 2 of 4
LOC105374754	XR_940128.3	n.1617+14531G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233891	ENST00000412409.3	n.546-128990G>A		intron_variant	Intron 4 of 4	3
ENSG00000233891	ENST00000434611.1	n.98+17969G>A		intron_variant	Intron 1 of 3	3
ENSG00000233891	ENST00000440521.6	n.183+17969G>A		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137060 AN: 151556 Hom.: 62101 Cov.: 31

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.904 AC: 137166 AN: 151674 Hom.: 62152 Cov.: 31 AF XY: 0.904 AC XY: 67017 AN XY: 74150

African (AFR) AF: 0.938 AC: 38936 AN: 41516

American (AMR) AF: 0.937 AC: 14238 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3253 AN: 3462

East Asian (EAS) AF: 0.993 AC: 5140 AN: 5178

South Asian (SAS) AF: 0.899 AC: 4331 AN: 4816

European-Finnish (FIN) AF: 0.833 AC: 8821 AN: 10592

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59411 AN: 67602

Other (OTH) AF: 0.915 AC: 1926 AN: 2106

Alfa AF: 0.889 Hom.: 31123

Bravo AF: 0.914

Asia WGS AF: 0.939 AC: 3264 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.57
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2192574; hg19: chr2-59597228;