chr1-245087293-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032328.4(EFCAB2):c.422T>C(p.Ile141Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000826 in 1,611,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032328.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000368 AC: 56AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000117 AC: 29AN: 247778Hom.: 0 AF XY: 0.0000969 AC XY: 13AN XY: 134182
GnomAD4 exome AF: 0.0000521 AC: 76AN: 1458770Hom.: 0 Cov.: 31 AF XY: 0.0000441 AC XY: 32AN XY: 725770
GnomAD4 genome AF: 0.000374 AC: 57AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.422T>C (p.I141T) alteration is located in exon 8 (coding exon 7) of the EFCAB2 gene. This alteration results from a T to C substitution at nucleotide position 422, causing the isoleucine (I) at amino acid position 141 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