rs10134675
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138420.4(AHNAK2):c.6559A>T(p.Met2187Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 24)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AHNAK2
NM_138420.4 missense
NM_138420.4 missense
Scores
19
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.85
Genes affected
AHNAK2 (HGNC:20125): (AHNAK nucleoprotein 2) This gene encodes a large nucleoprotein. The encoded protein has a tripartite domain structure with a relatively short N-terminus and a long C-terminus, separated by a large body of repeats. The N-terminal PSD-95/Discs-large/ZO-1 (PDZ)-like domain is thought to function in the formation of stable homodimers. The encoded protein may play a role in calcium signaling by associating with calcium channel proteins. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.025747746).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| AHNAK2 | NM_138420.4 | c.6559A>T | p.Met2187Leu | missense_variant | Exon 7 of 7 | ENST00000333244.6 | NP_612429.2 | |
| AHNAK2 | NM_001350929.2 | c.6259A>T | p.Met2087Leu | missense_variant | Exon 7 of 7 | NP_001337858.1 | ||
| AHNAK2 | XM_024449463.2 | c.6259A>T | p.Met2087Leu | missense_variant | Exon 7 of 7 | XP_024305231.1 | ||
| AHNAK2 | XM_047430904.1 | c.6259A>T | p.Met2087Leu | missense_variant | Exon 7 of 7 | XP_047286860.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| AHNAK2 | ENST00000333244.6 | c.6559A>T | p.Met2187Leu | missense_variant | Exon 7 of 7 | 5 | NM_138420.4 | ENSP00000353114.4 | ||
| AHNAK2 | ENST00000557457.1 | c.-221+4989A>T | intron_variant | Intron 1 of 2 | 1 | ENSP00000450998.1 | ||||
| AHNAK2 | ENST00000555122.1 | n.6687A>T | non_coding_transcript_exon_variant | Exon 6 of 6 | 5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
24
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.88e-7 AC: 1AN: 1453368Hom.: 0 Cov.: 114 AF XY: 0.00000138 AC XY: 1AN XY: 723030
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
1453368
Hom.:
Cov.:
114
AF XY:
AC XY:
1
AN XY:
723030
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome
GnomAD4 genome
Cov.:
24
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of catalytic residue at P2190 (P = 0.0261);
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at