6-138429778-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001144060.2(NHSL1):c.4018G>A(p.Gly1340Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000625 in 1,551,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHSL1 | ENST00000343505.10 | c.4018G>A | p.Gly1340Arg | missense_variant | Exon 7 of 8 | 5 | NM_001144060.2 | ENSP00000344672.5 | ||
NHSL1 | ENST00000427025.6 | c.4030G>A | p.Gly1344Arg | missense_variant | Exon 6 of 7 | 5 | ENSP00000394546.2 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000127 AC: 2AN: 157112Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 83172
GnomAD4 exome AF: 0.0000600 AC: 84AN: 1399522Hom.: 0 Cov.: 31 AF XY: 0.0000579 AC XY: 40AN XY: 690272
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4030G>A (p.G1344R) alteration is located in exon 6 (coding exon 6) of the NHSL1 gene. This alteration results from a G to A substitution at nucleotide position 4030, causing the glycine (G) at amino acid position 1344 to be replaced by an arginine (R). 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