ENST00000412409.3:n.261+42146C>T

Variant names:

• chr2-59677430-G-A
• rs1372878
• ENST00000412409.3:n.261+42146C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412409.3(ENSG00000233891):​n.261+42146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 152,202 control chromosomes in the GnomAD database, including 606 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 0.063 (606 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000412409.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

ENSG00000233891 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 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
ENSG00000233891	ENST00000412409.3	n.261+42146C>T		intron_variant	Intron 2 of 4	3
ENSG00000233891	ENST00000435557.1	n.224-7882C>T		intron_variant	Intron 2 of 2	4
ENSG00000271955	ENST00000606382.1	n.236+149716C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0633 AC: 9621 AN: 152084 Hom.: 605 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0633 AC: 9635 AN: 152202 Hom.: 606 Cov.: 32 AF XY: 0.0653 AC XY: 4860 AN XY: 74420

Gnomad4 AFR AF: 0.0873

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0338

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0429 Hom.: 146

Bravo AF: 0.0679

Asia WGS AF: 0.173 AC: 599 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372878; hg19: chr2-59904565;