chr11-20847704-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006157.5(NELL1):c.457G>A(p.Ala153Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00473 in 1,613,536 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0041 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0048 ( 30 hom. )
Consequence
NELL1
NM_006157.5 missense
NM_006157.5 missense
Scores
2
7
8
Clinical Significance
Conservation
PhyloP100: 6.74
Genes affected
NELL1 (HGNC:7750): (neural EGFL like 1) This gene encodes a cytoplasmic protein that contains epidermal growth factor (EGF)-like repeats. The encoded heterotrimeric protein may be involved in cell growth regulation and differentiation. A similar protein in rodents is involved in craniosynostosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010790795).
BP6
?
Variant 11-20847704-G-A is Benign according to our data. Variant chr11-20847704-G-A is described in ClinVar as [Benign]. Clinvar id is 719361.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NELL1 | NM_006157.5 | c.457G>A | p.Ala153Thr | missense_variant | 4/20 | ENST00000357134.10 | |
NELL1 | NM_001288713.1 | c.541G>A | p.Ala181Thr | missense_variant | 5/21 | ||
NELL1 | NM_201551.2 | c.457G>A | p.Ala153Thr | missense_variant | 4/19 | ||
NELL1 | NM_001288714.1 | c.336-37740G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NELL1 | ENST00000357134.10 | c.457G>A | p.Ala153Thr | missense_variant | 4/20 | 1 | NM_006157.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00411 AC: 625AN: 152184Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.00381 AC: 953AN: 250384Hom.: 4 AF XY: 0.00372 AC XY: 503AN XY: 135282
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GnomAD4 exome AF: 0.00480 AC: 7013AN: 1461234Hom.: 30 Cov.: 31 AF XY: 0.00453 AC XY: 3295AN XY: 726880
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GnomAD4 genome ? AF: 0.00410 AC: 625AN: 152302Hom.: 3 Cov.: 33 AF XY: 0.00475 AC XY: 354AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Pathogenic
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
0.86, 0.98
.;P;D
Vest4
MVP
MPC
0.43
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at