chr1-15410102-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024329.6(EFHD2):c.131C>T(p.Ala44Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 1,471,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024329.6 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 |
---|---|---|---|---|---|---|---|
EFHD2 | NM_024329.6 | c.131C>T | p.Ala44Val | missense_variant | 1/4 | ENST00000375980.9 | |
EFHD2-AS1 | NR_183705.1 | n.463+1804G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFHD2 | ENST00000375980.9 | c.131C>T | p.Ala44Val | missense_variant | 1/4 | 1 | NM_024329.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000725 AC: 11AN: 151660Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 4AN: 91210Hom.: 0 AF XY: 0.0000376 AC XY: 2AN XY: 53214
GnomAD4 exome AF: 0.0000159 AC: 21AN: 1319438Hom.: 0 Cov.: 32 AF XY: 0.0000107 AC XY: 7AN XY: 652020
GnomAD4 genome AF: 0.0000791 AC: 12AN: 151770Hom.: 0 Cov.: 32 AF XY: 0.0000809 AC XY: 6AN XY: 74184
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2022 | The c.131C>T (p.A44V) alteration is located in exon 1 (coding exon 1) of the EFHD2 gene. This alteration results from a C to T substitution at nucleotide position 131, causing the alanine (A) at amino acid position 44 to be replaced by a valine (V). 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