14-104938705-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_138420.4(AHNAK2):ā€‹c.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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.827
Variant links:
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
AHNAK2NM_138420.4 linkuse as main transcriptc.16746T>C p.Asn5582= synonymous_variant 7/7 ENST00000333244.6
AHNAK2NM_001350929.2 linkuse as main transcriptc.16446T>C p.Asn5482= synonymous_variant 7/7
AHNAK2XM_024449463.2 linkuse as main transcriptc.16446T>C p.Asn5482= synonymous_variant 7/7
AHNAK2XM_047430904.1 linkuse as main transcriptc.16446T>C p.Asn5482= synonymous_variant 7/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AHNAK2ENST00000333244.6 linkuse as main transcriptc.16746T>C p.Asn5582= synonymous_variant 7/75 NM_138420.4 P1Q8IVF2-1
AHNAK2ENST00000557457.1 linkuse as main transcriptc.1740T>C p.Asn580= synonymous_variant 3/31 Q8IVF2-2
AHNAK2ENST00000555122.1 linkuse as main transcriptn.16874T>C non_coding_transcript_exon_variant 6/65

Frequencies

GnomAD3 genomes
AF:
0.000184
AC:
28
AN:
152146
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000965
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00105
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000137
AC:
34
AN:
247702
Hom.:
0
AF XY:
0.000149
AC XY:
20
AN XY:
134542
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000611
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000929
Gnomad NFE exome
AF:
0.0000892
Gnomad OTH exome
AF:
0.000166
GnomAD4 exome
AF:
0.000196
AC:
286
AN:
1461168
Hom.:
0
Cov.:
73
AF XY:
0.000184
AC XY:
134
AN XY:
726788
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000627
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.000113
Gnomad4 NFE exome
AF:
0.000205
Gnomad4 OTH exome
AF:
0.000381
GnomAD4 genome
AF:
0.000184
AC:
28
AN:
152264
Hom.:
0
Cov.:
32
AF XY:
0.000148
AC XY:
11
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.0000963
Gnomad4 AMR
AF:
0.00105
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000147
Hom.:
0
Bravo
AF:
0.000325
EpiCase
AF:
0.000327
EpiControl
AF:
0.000238

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenApr 01, 2022AHNAK2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.14
DANN
Benign
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201233696; hg19: chr14-105405042; API