14-104938705-A-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_138420.4(AHNAK2):āc.16746T>Cā(p.Asn5582=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,613,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00018 ( 0 hom., cov: 32)
Exomes š: 0.00020 ( 0 hom. )
Consequence
AHNAK2
NM_138420.4 synonymous
NM_138420.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.827
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
Variant 14-104938705-A-G is Benign according to our data. Variant chr14-104938705-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2644629.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AHNAK2 | NM_138420.4 | c.16746T>C | p.Asn5582= | synonymous_variant | 7/7 | ENST00000333244.6 | |
AHNAK2 | NM_001350929.2 | c.16446T>C | p.Asn5482= | synonymous_variant | 7/7 | ||
AHNAK2 | XM_024449463.2 | c.16446T>C | p.Asn5482= | synonymous_variant | 7/7 | ||
AHNAK2 | XM_047430904.1 | c.16446T>C | p.Asn5482= | synonymous_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHNAK2 | ENST00000333244.6 | c.16746T>C | p.Asn5582= | synonymous_variant | 7/7 | 5 | NM_138420.4 | P1 | |
AHNAK2 | ENST00000557457.1 | c.1740T>C | p.Asn580= | synonymous_variant | 3/3 | 1 | |||
AHNAK2 | ENST00000555122.1 | n.16874T>C | non_coding_transcript_exon_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152146Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000137 AC: 34AN: 247702Hom.: 0 AF XY: 0.000149 AC XY: 20AN XY: 134542
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GnomAD4 exome AF: 0.000196 AC: 286AN: 1461168Hom.: 0 Cov.: 73 AF XY: 0.000184 AC XY: 134AN XY: 726788
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GnomAD4 genome AF: 0.000184 AC: 28AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74450
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | AHNAK2: BP4, BP7 - |
Computational scores
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CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at