chr6-138424487-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001144060.2(NHSL1):c.4415A>G(p.Asn1472Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 1,551,388 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NHSL1 | NM_001144060.2 | c.4415A>G | p.Asn1472Ser | missense_variant | 8/8 | ENST00000343505.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHSL1 | ENST00000343505.10 | c.4415A>G | p.Asn1472Ser | missense_variant | 8/8 | 5 | NM_001144060.2 | P3 | |
NHSL1 | ENST00000427025.6 | c.4427A>G | p.Asn1476Ser | missense_variant | 7/7 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152004Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000387 AC: 6AN: 155032Hom.: 0 AF XY: 0.0000365 AC XY: 3AN XY: 82246
GnomAD4 exome AF: 0.0000286 AC: 40AN: 1399384Hom.: 0 Cov.: 33 AF XY: 0.0000261 AC XY: 18AN XY: 690198
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152004Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.4427A>G (p.N1476S) alteration is located in exon 7 (coding exon 7) of the NHSL1 gene. This alteration results from a A to G substitution at nucleotide position 4427, causing the asparagine (N) at amino acid position 1476 to be replaced by a serine (S). 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