13-110879702-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_017664.4(ANKRD10):​c.1198G>C​(p.Val400Leu) 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

ANKRD10
NM_017664.4 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.11
Variant links:
Genes affected
ANKRD10 (HGNC:20265): (ankyrin repeat domain 10)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.26315182).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ANKRD10NM_017664.4 linkc.1198G>C p.Val400Leu missense_variant Exon 6 of 6 ENST00000267339.6 NP_060134.2 Q9NXR5-1A0A024RE01
ANKRD10XM_024449380.2 linkc.*395G>C 3_prime_UTR_variant Exon 6 of 6 XP_024305148.1
ANKRD10NR_104587.2 linkn.1395G>C non_coding_transcript_exon_variant Exon 7 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ANKRD10ENST00000267339.6 linkc.1198G>C p.Val400Leu missense_variant Exon 6 of 6 2 NM_017664.4 ENSP00000267339.2 Q9NXR5-1
ANKRD10ENST00000485844.1 linkn.*66G>C downstream_gene_variant 2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 14, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1198G>C (p.V400L) alteration is located in exon 6 (coding exon 6) of the ANKRD10 gene. This alteration results from a G to C substitution at nucleotide position 1198, causing the valine (V) at amino acid position 400 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
0.0023
T
BayesDel_noAF
Benign
-0.23
CADD
Benign
17
DANN
Benign
0.97
DEOGEN2
Benign
0.067
T
Eigen
Benign
-0.046
Eigen_PC
Benign
-0.11
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.69
T
M_CAP
Uncertain
0.24
D
MetaRNN
Benign
0.26
T
MetaSVM
Benign
-0.31
T
MutationAssessor
Uncertain
2.3
M
PrimateAI
Benign
0.45
T
PROVEAN
Benign
-1.2
N
REVEL
Uncertain
0.32
Sift
Uncertain
0.0040
D
Sift4G
Benign
0.20
T
Polyphen
0.79
P
Vest4
0.33
MutPred
0.28
Gain of loop (P = 0.0045);
MVP
0.73
MPC
0.52
ClinPred
0.69
D
GERP RS
4.0
Varity_R
0.10
gMVP
0.36

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr13-111532049; API