Given REF is incompatible with our hg38 reference sequence (T). Please double check if it's correct.

1-342342-A-C (hg19)

Lifted to hg38:1-476995-A-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000796423.1(ENSG00000290385):​n.586-50T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 0)
• Consequence: ENSG00000290385 ENST00000796423.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

Genes affected

ENSG00000290385 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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
ENSG00000290385	ENST00000455207.5	n.169+8045T>G		intron_variant	Intron 1 of 2	5
ENSG00000290385	ENST00000455464.7	n.321-50T>G		intron_variant	Intron 2 of 2	5
ENSG00000290385	ENST00000796423.1	n.586-50T>G		intron_variant	Intron 5 of 5
ENSG00000290385	ENST00000796424.1	n.267-50T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.0
DANN	Benign	0.28
PhyloP100		-0.12

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-180768957;