X-63350199-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001012968.3(SPIN4):c.621T>A(p.His207Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,209,973 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001012968.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000358 AC: 4AN: 111745Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33935
GnomAD3 exomes AF: 0.0000605 AC: 11AN: 181833Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67657
GnomAD4 exome AF: 0.0000127 AC: 14AN: 1098175Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363533
GnomAD4 genome AF: 0.0000358 AC: 4AN: 111798Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33998
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.621T>A (p.H207Q) alteration is located in exon 1 (coding exon 1) of the SPIN4 gene. This alteration results from a T to A substitution at nucleotide position 621, causing the histidine (H) at amino acid position 207 to be replaced by a glutamine (Q). 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