19-19634670-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_016573.4(GMIP):c.1921G>A(p.Asp641Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0344 in 1,611,504 control chromosomes in the GnomAD database, including 1,098 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_016573.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GMIP | NM_016573.4 | c.1921G>A | p.Asp641Asn | missense_variant | Exon 18 of 21 | ENST00000203556.9 | NP_057657.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GMIP | ENST00000203556.9 | c.1921G>A | p.Asp641Asn | missense_variant | Exon 18 of 21 | 1 | NM_016573.4 | ENSP00000203556.3 | ||
GMIP | ENST00000587238.5 | c.1843G>A | p.Asp615Asn | missense_variant | Exon 17 of 20 | 1 | ENSP00000467054.1 | |||
GMIP | ENST00000586269.1 | n.453+122G>A | intron_variant | Intron 3 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0268 AC: 4070AN: 151914Hom.: 91 Cov.: 32
GnomAD3 exomes AF: 0.0298 AC: 7454AN: 249804Hom.: 150 AF XY: 0.0307 AC XY: 4140AN XY: 135066
GnomAD4 exome AF: 0.0352 AC: 51387AN: 1459472Hom.: 1007 Cov.: 34 AF XY: 0.0350 AC XY: 25373AN XY: 725758
GnomAD4 genome AF: 0.0268 AC: 4069AN: 152032Hom.: 91 Cov.: 32 AF XY: 0.0269 AC XY: 2000AN XY: 74312
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at