17-48610588-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004502.4(HOXB7):c.331A>G(p.Lys111Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000516 in 1,550,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004502.4 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: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000258 AC: 4AN: 155244Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83258
GnomAD4 exome AF: 0.00000501 AC: 7AN: 1397902Hom.: 0 Cov.: 31 AF XY: 0.00000435 AC XY: 3AN XY: 689460
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.331A>G (p.K111E) alteration is located in exon 1 (coding exon 1) of the HOXB7 gene. This alteration results from a A to G substitution at nucleotide position 331, causing the lysine (K) at amino acid position 111 to be replaced by a glutamic acid (E). 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