chr1-160950641-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_080878.3(ITLN2):āc.512A>Gā(p.Gln171Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00557 in 1,614,204 control chromosomes in the GnomAD database, including 427 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 Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_080878.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITLN2 | NM_080878.3 | c.512A>G | p.Gln171Arg | missense_variant | 5/8 | ENST00000368029.4 | |
ITLN2 | XM_024453321.2 | c.509A>G | p.Gln170Arg | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITLN2 | ENST00000368029.4 | c.512A>G | p.Gln171Arg | missense_variant | 5/8 | 1 | NM_080878.3 | P1 | |
ITLN2 | ENST00000490489.1 | n.503A>G | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
ITLN2 | ENST00000494442.1 | n.372A>G | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0295 AC: 4486AN: 152216Hom.: 235 Cov.: 32
GnomAD3 exomes AF: 0.00790 AC: 1987AN: 251362Hom.: 94 AF XY: 0.00567 AC XY: 770AN XY: 135858
GnomAD4 exome AF: 0.00308 AC: 4501AN: 1461870Hom.: 192 Cov.: 31 AF XY: 0.00257 AC XY: 1872AN XY: 727242
GnomAD4 genome AF: 0.0295 AC: 4497AN: 152334Hom.: 235 Cov.: 32 AF XY: 0.0283 AC XY: 2108AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at