1-67430116-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001018069.2(SERBP1):c.185A>C(p.Asn62Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,612,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001018069.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERBP1 | NM_001018069.2 | c.185A>C | p.Asn62Thr | missense_variant | 1/8 | ENST00000361219.11 | |
SERBP1 | NM_001018067.2 | c.185A>C | p.Asn62Thr | missense_variant | 1/8 | ||
SERBP1 | NM_001018068.2 | c.185A>C | p.Asn62Thr | missense_variant | 1/8 | ||
SERBP1 | NM_015640.4 | c.185A>C | p.Asn62Thr | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERBP1 | ENST00000361219.11 | c.185A>C | p.Asn62Thr | missense_variant | 1/8 | 1 | NM_001018069.2 | ||
SERBP1 | ENST00000370995.6 | c.185A>C | p.Asn62Thr | missense_variant | 1/8 | 1 | P3 | ||
SERBP1 | ENST00000370990.5 | c.185A>C | p.Asn62Thr | missense_variant | 1/8 | 1 | A1 | ||
SERBP1 | ENST00000370994.8 | c.185A>C | p.Asn62Thr | missense_variant | 1/8 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248722Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135086
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1459898Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726216
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2023 | The c.185A>C (p.N62T) alteration is located in exon 1 (coding exon 1) of the SERBP1 gene. This alteration results from a A to C substitution at nucleotide position 185, causing the asparagine (N) at amino acid position 62 to be replaced by a threonine (T). 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