6-138424548-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001144060.2(NHSL1):c.4354T>A(p.Ser1452Thr) 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 1,551,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144060.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHSL1 | NM_001144060.2 | c.4354T>A | p.Ser1452Thr | missense_variant | 8/8 | ENST00000343505.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHSL1 | ENST00000343505.10 | c.4354T>A | p.Ser1452Thr | missense_variant | 8/8 | 5 | NM_001144060.2 | P3 | |
NHSL1 | ENST00000427025.6 | c.4366T>A | p.Ser1456Thr | missense_variant | 7/7 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151596Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000256 AC: 4AN: 156218Hom.: 0 AF XY: 0.0000241 AC XY: 2AN XY: 82822
GnomAD4 exome AF: 0.0000164 AC: 23AN: 1399410Hom.: 0 Cov.: 33 AF XY: 0.0000145 AC XY: 10AN XY: 690214
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151596Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74018
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 30, 2023 | The c.4366T>A (p.S1456T) alteration is located in exon 7 (coding exon 7) of the NHSL1 gene. This alteration results from a T to A substitution at nucleotide position 4366, causing the serine (S) at amino acid position 1456 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