7-102638756-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001114403.3(UPK3BL1):c.641C>T(p.Ala214Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001114403.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UPK3BL1 | ENST00000340457.8 | c.641C>T | p.Ala214Val | missense_variant | Exon 5 of 6 | 1 | NM_001114403.3 | ENSP00000342938.8 | ||
ENSG00000267645 | ENST00000476151.5 | n.*583C>T | non_coding_transcript_exon_variant | Exon 8 of 9 | 1 | ENSP00000418603.1 | ||||
ENSG00000205236 | ENST00000519541.1 | n.641C>T | non_coding_transcript_exon_variant | Exon 5 of 26 | 2 | ENSP00000429397.1 | ||||
ENSG00000267645 | ENST00000476151.5 | n.*583C>T | 3_prime_UTR_variant | Exon 8 of 9 | 1 | ENSP00000418603.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 4AN: 148528Hom.: 0 Cov.: 25 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000148 AC: 15AN: 1010940Hom.: 0 Cov.: 16 AF XY: 0.0000200 AC XY: 10AN XY: 500660
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000269 AC: 4AN: 148528Hom.: 0 Cov.: 25 AF XY: 0.0000277 AC XY: 2AN XY: 72294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.641C>T (p.A214V) alteration is located in exon 5 (coding exon 5) of the UPK3BL gene. This alteration results from a C to T substitution at nucleotide position 641, causing the alanine (A) at amino acid position 214 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at