6-138430861-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001144060.2(NHSL1):c.3484C>T(p.Arg1162Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000961 in 1,550,972 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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.3484C>T | p.Arg1162Cys | missense_variant | 6/8 | ENST00000343505.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NHSL1 | ENST00000343505.10 | c.3484C>T | p.Arg1162Cys | missense_variant | 6/8 | 5 | NM_001144060.2 | P3 | |
NHSL1 | ENST00000427025.6 | c.3496C>T | p.Arg1166Cys | missense_variant | 5/7 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000110 AC: 17AN: 154504Hom.: 0 AF XY: 0.0000609 AC XY: 5AN XY: 82082
GnomAD4 exome AF: 0.0000994 AC: 139AN: 1398708Hom.: 1 Cov.: 34 AF XY: 0.000101 AC XY: 70AN XY: 689798
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.3496C>T (p.R1166C) alteration is located in exon 5 (coding exon 5) of the NHSL1 gene. This alteration results from a C to T substitution at nucleotide position 3496, causing the arginine (R) at amino acid position 1166 to be replaced by a cysteine (C). 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