7-150628087-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024711.6(GIMAP6):c.511G>A(p.Gly171Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,614,018 control chromosomes in the GnomAD database, including 36,116 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_024711.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GIMAP6 | NM_024711.6 | c.511G>A | p.Gly171Ser | missense_variant | Exon 3 of 3 | ENST00000328902.9 | NP_078987.3 | |
GIMAP6 | NM_001244072.2 | c.721G>A | p.Gly241Ser | missense_variant | Exon 3 of 3 | NP_001231001.1 | ||
GIMAP6 | NM_001244071.2 | c.*98G>A | 3_prime_UTR_variant | Exon 3 of 3 | NP_001231000.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GIMAP6 | ENST00000328902.9 | c.511G>A | p.Gly171Ser | missense_variant | Exon 3 of 3 | 1 | NM_024711.6 | ENSP00000330374.5 | ||
GIMAP6 | ENST00000618759.4 | c.721G>A | p.Gly241Ser | missense_variant | Exon 3 of 3 | 2 | ENSP00000479580.1 | |||
GIMAP6 | ENST00000493969 | c.*98G>A | 3_prime_UTR_variant | Exon 3 of 3 | 2 | ENSP00000418304.1 |
Frequencies
GnomAD3 genomes AF: 0.183 AC: 27864AN: 152054Hom.: 2998 Cov.: 33
GnomAD3 exomes AF: 0.221 AC: 55397AN: 251068Hom.: 6655 AF XY: 0.221 AC XY: 29929AN XY: 135682
GnomAD4 exome AF: 0.209 AC: 305913AN: 1461846Hom.: 33121 Cov.: 37 AF XY: 0.209 AC XY: 152160AN XY: 727218
GnomAD4 genome AF: 0.183 AC: 27864AN: 152172Hom.: 2995 Cov.: 33 AF XY: 0.189 AC XY: 14091AN XY: 74386
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 48% of patients studied by a panel of primary immunodeficiencies. Number of patients: 46. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at