chr2-200981659-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001321623.1(HYCC2):c.1372T>G(p.Ser458Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001321623.1 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 |
---|---|---|---|---|---|---|---|
HYCC2 | NM_001321623.1 | c.1372T>G | p.Ser458Ala | missense_variant | 13/13 | ENST00000681958.1 | |
LOC105373835 | XR_007088050.1 | n.199+18029A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYCC2 | ENST00000681958.1 | c.1372T>G | p.Ser458Ala | missense_variant | 13/13 | NM_001321623.1 | P3 | ||
HYCC2 | ENST00000418596.7 | c.1204T>G | p.Ser402Ala | missense_variant | 12/12 | 1 | A1 | ||
HYCC2 | ENST00000286181.7 | c.*1125T>G | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | 1 | ||||
ENST00000413848.1 | n.368+18029A>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251338Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135840
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727246
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74250
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2023 | The c.1204T>G (p.S402A) alteration is located in exon 12 (coding exon 10) of the FAM126B gene. This alteration results from a T to G substitution at nucleotide position 1204, causing the serine (S) at amino acid position 402 to be replaced by an alanine (A). 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