rs2074381
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_025144.4(ALPK1):āc.2746A>Gā(p.Asn916Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00395 in 1,614,202 control chromosomes in the GnomAD database, including 163 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_025144.4 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALPK1 | NM_025144.4 | c.2746A>G | p.Asn916Asp | missense_variant | 11/16 | ENST00000650871.1 | NP_079420.3 | |
ALPK1 | NM_001102406.2 | c.2746A>G | p.Asn916Asp | missense_variant | 11/16 | NP_001095876.1 | ||
ALPK1 | NM_001253884.2 | c.2512A>G | p.Asn838Asp | missense_variant | 10/15 | NP_001240813.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALPK1 | ENST00000650871.1 | c.2746A>G | p.Asn916Asp | missense_variant | 11/16 | NM_025144.4 | ENSP00000498374.1 |
Frequencies
GnomAD3 genomes AF: 0.00620 AC: 943AN: 152194Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.00845 AC: 2124AN: 251300Hom.: 48 AF XY: 0.00830 AC XY: 1127AN XY: 135804
GnomAD4 exome AF: 0.00371 AC: 5427AN: 1461890Hom.: 143 Cov.: 35 AF XY: 0.00368 AC XY: 2674AN XY: 727244
GnomAD4 genome AF: 0.00621 AC: 946AN: 152312Hom.: 20 Cov.: 32 AF XY: 0.00835 AC XY: 622AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at