1-210238070-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019605.5(SERTAD4):c.110C>T(p.Pro37Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,613,680 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019605.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SERTAD4 | NM_019605.5 | c.110C>T | p.Pro37Leu | missense_variant | Exon 2 of 4 | ENST00000367012.4 | NP_062551.1 | |
SERTAD4 | NM_001375428.1 | c.110C>T | p.Pro37Leu | missense_variant | Exon 2 of 4 | NP_001362357.1 | ||
SERTAD4 | NM_001354173.2 | c.110C>T | p.Pro37Leu | missense_variant | Exon 2 of 5 | NP_001341102.1 | ||
SERTAD4 | XM_047425536.1 | c.110C>T | p.Pro37Leu | missense_variant | Exon 2 of 5 | XP_047281492.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERTAD4 | ENST00000367012.4 | c.110C>T | p.Pro37Leu | missense_variant | Exon 2 of 4 | 1 | NM_019605.5 | ENSP00000355979.3 | ||
SERTAD4 | ENST00000482421.1 | n.128C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 3 | |||||
SERTAD4 | ENST00000483884.1 | n.93C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 | |||||
SERTAD4 | ENST00000490620.5 | n.314C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251128Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135744
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461472Hom.: 0 Cov.: 34 AF XY: 0.0000426 AC XY: 31AN XY: 727080
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.110C>T (p.P37L) alteration is located in exon 2 (coding exon 1) of the SERTAD4 gene. This alteration results from a C to T substitution at nucleotide position 110, causing the proline (P) at amino acid position 37 to be replaced by a leucine (L). 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