4-127808093-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014278.4(HSPA4L):āc.1342A>Cā(p.Asn448His) 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 1,611,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014278.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA4L | NM_014278.4 | c.1342A>C | p.Asn448His | missense_variant | 11/19 | ENST00000296464.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA4L | ENST00000296464.9 | c.1342A>C | p.Asn448His | missense_variant | 11/19 | 1 | NM_014278.4 | P1 | |
HSPA4L | ENST00000508549.5 | c.1219A>C | p.Asn407His | missense_variant | 10/13 | 1 | |||
HSPA4L | ENST00000508776.5 | c.1342A>C | p.Asn448His | missense_variant | 12/20 | 2 | P1 | ||
HSPA4L | ENST00000505726.1 | c.1264A>C | p.Asn422His | missense_variant | 11/19 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248012Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133920
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1459666Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 726090
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2023 | The c.1342A>C (p.N448H) alteration is located in exon 11 (coding exon 11) of the HSPA4L gene. This alteration results from a A to C substitution at nucleotide position 1342, causing the asparagine (N) at amino acid position 448 to be replaced by a histidine (H). 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