NM_198510.3:c.3517C>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_198510.3(ITIH6):c.3517C>T(p.Arg1173Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,210,228 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. 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_198510.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000535 AC: 6AN: 112193Hom.: 0 Cov.: 22 AF XY: 0.0000291 AC XY: 1AN XY: 34353
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 182793Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67307
GnomAD4 exome AF: 0.0000118 AC: 13AN: 1098035Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 2AN XY: 363389
GnomAD4 genome AF: 0.0000535 AC: 6AN: 112193Hom.: 0 Cov.: 22 AF XY: 0.0000291 AC XY: 1AN XY: 34353
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3517C>T (p.R1173C) alteration is located in exon 12 (coding exon 12) of the ITIH6 gene. This alteration results from a C to T substitution at nucleotide position 3517, causing the arginine (R) at amino acid position 1173 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