chr10-90857666-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_019859.4(HTR7):c.6G>A(p.Met2Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,568,318 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019859.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR7 | NM_019859.4 | c.6G>A | p.Met2Ile | missense_variant | 1/4 | ENST00000336152.8 | |
HTR7 | NM_000872.5 | c.6G>A | p.Met2Ile | missense_variant | 1/3 | ||
HTR7 | NM_019860.4 | c.6G>A | p.Met2Ile | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR7 | ENST00000336152.8 | c.6G>A | p.Met2Ile | missense_variant | 1/4 | 1 | NM_019859.4 | ||
HTR7 | ENST00000277874.10 | c.6G>A | p.Met2Ile | missense_variant | 1/3 | 1 | A1 | ||
HTR7 | ENST00000371719.2 | c.6G>A | p.Met2Ile | missense_variant | 1/3 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 22AN: 172176Hom.: 0 AF XY: 0.000134 AC XY: 13AN XY: 96698
GnomAD4 exome AF: 0.000186 AC: 263AN: 1416106Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 123AN XY: 702682
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.6G>A (p.M2I) alteration is located in exon 1 (coding exon 1) of the HTR7 gene. This alteration results from a G to A substitution at nucleotide position 6, causing the methionine (M) at amino acid position 2 to be replaced by an isoleucine (I). 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