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GeneBe

rs10994336

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000373827.6(ANK3):c.97-140415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0797 in 152,064 control chromosomes in the GnomAD database, including 910 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.080 ( 910 hom., cov: 32)

Consequence

ANK3
ENST00000373827.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.705
Variant links:
Genes affected
ANK3 (HGNC:494): (ankyrin 3) Ankyrins are a family of proteins that are believed to link the integral membrane proteins to the underlying spectrin-actin cytoskeleton and play key roles in activities such as cell motility, activation, proliferation, contact, and the maintenance of specialized membrane domains. Multiple isoforms of ankyrin with different affinities for various target proteins are expressed in a tissue-specific, developmentally regulated manner. Most ankyrins are typically composed of three structural domains: an amino-terminal domain containing multiple ankyrin repeats; a central region with a highly conserved spectrin binding domain; and a carboxy-terminal regulatory domain which is the least conserved and subject to variation. Ankyrin 3 is an immunologically distinct gene product from ankyrins 1 and 2, and was originally found at the axonal initial segment and nodes of Ranvier of neurons in the central and peripheral nervous systems. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ANK3NM_001204403.2 linkuse as main transcriptc.97-140415G>A intron_variant
ANK3NM_001204404.2 linkuse as main transcriptc.64-140415G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANK3ENST00000373827.6 linkuse as main transcriptc.97-140415G>A intron_variant 1 Q12955-5
ANK3ENST00000503366.6 linkuse as main transcriptc.64-140415G>A intron_variant 2 Q12955-4
ANK3ENST00000622427.4 linkuse as main transcriptc.64-140415G>A intron_variant, NMD_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0796
AC:
12101
AN:
151946
Hom.:
903
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0153
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.196
Gnomad ASJ
AF:
0.0447
Gnomad EAS
AF:
0.223
Gnomad SAS
AF:
0.144
Gnomad FIN
AF:
0.189
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0638
Gnomad OTH
AF:
0.0699
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0797
AC:
12114
AN:
152064
Hom.:
910
Cov.:
32
AF XY:
0.0895
AC XY:
6652
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.0153
Gnomad4 AMR
AF:
0.197
Gnomad4 ASJ
AF:
0.0447
Gnomad4 EAS
AF:
0.221
Gnomad4 SAS
AF:
0.142
Gnomad4 FIN
AF:
0.189
Gnomad4 NFE
AF:
0.0638
Gnomad4 OTH
AF:
0.0720
Alfa
AF:
0.0677
Hom.:
905
Bravo
AF:
0.0795
Asia WGS
AF:
0.194
AC:
672
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
6.2
Dann
Benign
0.67

Splicing

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: rs10994336; hg19: chr10-62179812; API