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GeneBe

6-34967290-C-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_015245.3(ANKS1A):c.249C>G(p.Pro83=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00289 in 1,613,992 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0030 ( 7 hom. )

Consequence

ANKS1A
NM_015245.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.853
Variant links:
Genes affected
ANKS1A (HGNC:20961): (ankyrin repeat and sterile alpha motif domain containing 1A) Predicted to enable ephrin receptor binding activity. Predicted to be involved in ephrin receptor signaling pathway; neuron remodeling; and substrate-dependent cell migration. Predicted to act upstream of or within negative regulation of ubiquitin-dependent protein catabolic process and regulation of ephrin receptor signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-34967290-C-G is Benign according to our data. Variant chr6-34967290-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3067220.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.853 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ANKS1ANM_015245.3 linkuse as main transcriptc.249C>G p.Pro83= synonymous_variant 2/24 ENST00000360359.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANKS1AENST00000360359.5 linkuse as main transcriptc.249C>G p.Pro83= synonymous_variant 2/241 NM_015245.3 Q92625-1
ANKS1AENST00000649117.1 linkuse as main transcriptc.249C>G p.Pro83= synonymous_variant 2/25 P1
ANKS1AENST00000650178.1 linkuse as main transcriptc.249C>G p.Pro83= synonymous_variant 2/10

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00177
AC:
269
AN:
152016
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000797
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000590
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00170
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00301
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.00154
AC:
386
AN:
251294
Hom.:
0
AF XY:
0.00152
AC XY:
206
AN XY:
135792
show subpopulations
Gnomad AFR exome
AF:
0.000984
Gnomad AMR exome
AF:
0.000578
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000294
Gnomad FIN exome
AF:
0.00152
Gnomad NFE exome
AF:
0.00262
Gnomad OTH exome
AF:
0.00163
GnomAD4 exome
AF:
0.00301
AC:
4403
AN:
1461858
Hom.:
7
Cov.:
32
AF XY:
0.00293
AC XY:
2131
AN XY:
727230
show subpopulations
Gnomad4 AFR exome
AF:
0.000538
Gnomad4 AMR exome
AF:
0.000984
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000301
Gnomad4 FIN exome
AF:
0.00150
Gnomad4 NFE exome
AF:
0.00366
Gnomad4 OTH exome
AF:
0.00263
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00177
AC:
269
AN:
152134
Hom.:
0
Cov.:
31
AF XY:
0.00160
AC XY:
119
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.000795
Gnomad4 AMR
AF:
0.000589
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00170
Gnomad4 NFE
AF:
0.00302
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00278
Hom.:
0
Bravo
AF:
0.00188
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00360
EpiControl
AF:
0.00308

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 TuebingenMar 01, 2024ANKS1A: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
Cadd
Benign
6.1
Dann
Benign
0.65
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs147758055; hg19: chr6-34935067; API