ENST00000759543.1:n.436-24165_436-23350del

Variant names:

• chr3-65132271-AATATCTACTAGATACTTTCCAAAGGGTTAATCAGCTTTAACATGGGGTGATGCCACTGTGCTGGTCTAAAATGTGTGATTTGCAGATGGAGGTTGGTGGGATCAACCACAAAGTCTGTCATCAAATGAAACACAAATGTGTTCACCTCTGGTCACTGGTTCAGGTTCTGGGCAGTCTGTCCCTTTGGCTGGAGGTAGAAGAACACTTTGGTAACTGTTGTGAGTGTGGTGGTGCAAGCTGAATAAGTTGATGTCCCCTTGGACTTCTATTTGAGATTTCTCCTCTGGTATTTTTATGGTACAGGTTTTGGGCAGTTGAATGAGAGTATGTAGGGACTGATCTTAGAAAACCAATGTAAGTCCAGGCATAGTGGCTCACACTTGTAATTCCAGCAGTTTGGGAGGCTGAGGCGAGTGGATCACTCAAGGTCAGGAGCTCGAGACCAGCCTGGCCAACATGATGAAACCCTGTCTCTACTAAAAATACAAAAATTATCTGGGCATGGTGACAGGCGCCTGTAGTCCCAGCTGCTTAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCAAGATCGCACCACTGCACTCCAGCCTCGGTGACAGAGCAACACTCCATCTCAAAAAAAAAAAAAAAGAAAAAAAAGAAAGAAAACCAACATAAATCAGACTGTTACCTTCTATCCCTTTTCCCTGTCTAATAGGAGGAGAATGCCCCCTCTTATAACCCATTTGCTATACCTCTGCCAGCAATCTTTCACACATGCAGCAGCTGAATTGTCACTTCTTCAAAGACAT-A
• rs1553673680
• ENST00000759543.1:n.436-24165_436-23350del

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000759543.1(ENSG00000298971):​n.436-24165_436-23350del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 31)
• Consequence: ENSG00000298971 ENST00000759543.1 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.827
• Publications: 0 publications found

Genes affected

ENSG00000298971 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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
ENSG00000298971	ENST00000759543.1	n.436-24165_436-23350del		intron_variant	Intron 3 of 4
ENSG00000298971	ENST00000759544.1	n.634-24165_634-23350del		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

Normal pregnancy Other:1

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Institute of Molecular and Cell Biology, University of Tartu

Significance: not provided

Review Status: no classification provided

Collection Method: case-control

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1553673680; hg19: chr3-65117946;