rs2941584

Variant summary

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

The NM_003128.3(SPTBN1):​c.5823-586T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,066 control chromosomes in the GnomAD database, including 31,424 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 0.64 ( 31424 hom., cov: 32)

Consequence

SPTBN1
NM_003128.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.67
Variant links:
Genes affected
SPTBN1 (HGNC:11275): (spectrin beta, non-erythrocytic 1) 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 contains an N-terminal actin-binding domain, and 17 spectrin repeats which are involved in dimer formation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SPTBN1NM_003128.3 linkuse as main transcriptc.5823-586T>C intron_variant ENST00000356805.9 NP_003119.2 Q01082-1B2ZZ89

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPTBN1ENST00000356805.9 linkuse as main transcriptc.5823-586T>C intron_variant 1 NM_003128.3 ENSP00000349259.4 Q01082-1
SPTBN1ENST00000333896.5 linkuse as main transcriptc.5784-586T>C intron_variant 1 ENSP00000334156.5 Q01082-3
SPTBN1ENST00000615901.4 linkuse as main transcriptc.5829-586T>C intron_variant 5 A0A087WUZ3
SPTBN1ENST00000496323.1 linkuse as main transcriptn.1337-586T>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.636
AC:
96599
AN:
151948
Hom.:
31408
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.535
Gnomad AMI
AF:
0.793
Gnomad AMR
AF:
0.690
Gnomad ASJ
AF:
0.534
Gnomad EAS
AF:
0.439
Gnomad SAS
AF:
0.570
Gnomad FIN
AF:
0.768
Gnomad MID
AF:
0.573
Gnomad NFE
AF:
0.688
Gnomad OTH
AF:
0.626
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.636
AC:
96663
AN:
152066
Hom.:
31424
Cov.:
32
AF XY:
0.636
AC XY:
47301
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.535
Gnomad4 AMR
AF:
0.690
Gnomad4 ASJ
AF:
0.534
Gnomad4 EAS
AF:
0.439
Gnomad4 SAS
AF:
0.570
Gnomad4 FIN
AF:
0.768
Gnomad4 NFE
AF:
0.688
Gnomad4 OTH
AF:
0.622
Alfa
AF:
0.666
Hom.:
44556
Bravo
AF:
0.625
Asia WGS
AF:
0.542
AC:
1885
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.17
DANN
Benign
0.51

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: rs2941584; hg19: chr2-54881621; API