19-41625646-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001817.4(CEACAM4):c.379G>A(p.Ala127Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,600,506 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_001817.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
CEACAM4 | ENST00000221954.7 | c.379G>A | p.Ala127Thr | missense_variant | Exon 2 of 7 | 1 | NM_001817.4 | ENSP00000221954.2 | ||
CEACAM4 | ENST00000600925.1 | c.379G>A | p.Ala127Thr | missense_variant | Exon 2 of 6 | 2 | ENSP00000473018.1 | |||
CEACAM4 | ENST00000472081.1 | n.490G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000414 AC: 1AN: 241530Hom.: 0 AF XY: 0.00000768 AC XY: 1AN XY: 130194
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1448426Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 719184
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.379G>A (p.A127T) alteration is located in exon 2 (coding exon 2) of the CEACAM4 gene. This alteration results from a G to A substitution at nucleotide position 379, causing the alanine (A) at amino acid position 127 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