19-40487509-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_020971.3(SPTBN4):c.170-188C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.08 in 150,090 control chromosomes in the GnomAD database, including 527 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.080 ( 527 hom., cov: 31)
Consequence
SPTBN4
NM_020971.3 intron
NM_020971.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.231
Genes affected
SPTBN4 (HGNC:14896): (spectrin beta, non-erythrocytic 4) Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. This gene is one member of a family of beta-spectrin genes. The encoded protein localizes to the nuclear matrix, PML nuclear bodies, and cytoplasmic vesicles. A highly similar gene in the mouse is required for localization of specific membrane proteins in polarized regions of neurons. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 19-40487509-C-T is Benign according to our data. Variant chr19-40487509-C-T is described in ClinVar as [Benign]. Clinvar id is 1278919.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPTBN4 | ENST00000598249.6 | c.170-188C>T | intron_variant | Intron 2 of 35 | 1 | NM_020971.3 | ENSP00000469242.1 | |||
SPTBN4 | ENST00000352632.7 | c.170-188C>T | intron_variant | Intron 2 of 35 | 5 | ENSP00000263373.2 | ||||
SPTBN4 | ENST00000595535.5 | c.170-188C>T | intron_variant | Intron 2 of 26 | 5 | ENSP00000470693.1 |
Frequencies
GnomAD3 genomes AF: 0.0800 AC: 11997AN: 149966Hom.: 525 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0800 AC: 12013AN: 150090Hom.: 527 Cov.: 31 AF XY: 0.0800 AC XY: 5867AN XY: 73348
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216
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 16, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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