rs11881477

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001111020.3(SUPT5H):​c.308-155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 1,292,858 control chromosomes in the GnomAD database, including 97,215 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 0.46 ( 18051 hom., cov: 28)
Exomes 𝑓: 0.36 ( 79164 hom. )

Consequence

SUPT5H
NM_001111020.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0230
Variant links:
Genes affected
SUPT5H (HGNC:11469): (SPT5 homolog, DSIF elongation factor subunit) Enables enzyme binding activity and protein heterodimerization activity. Involved in positive regulation of macroautophagy; regulation of RNA metabolic process; and transcription elongation from RNA polymerase II promoter. Located in nucleoplasm. Part of DSIF complex. [provided by Alliance of Genome Resources, Apr 2022]

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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 (BayesDel_noAF=-0.4).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SUPT5HNM_001111020.3 linkuse as main transcriptc.308-155G>A intron_variant ENST00000432763.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SUPT5HENST00000432763.7 linkuse as main transcriptc.308-155G>A intron_variant 1 NM_001111020.3 P1O00267-1

Frequencies

GnomAD3 genomes
AF:
0.462
AC:
69812
AN:
151052
Hom.:
18014
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.705
Gnomad AMI
AF:
0.281
Gnomad AMR
AF:
0.378
Gnomad ASJ
AF:
0.355
Gnomad EAS
AF:
0.516
Gnomad SAS
AF:
0.368
Gnomad FIN
AF:
0.405
Gnomad MID
AF:
0.402
Gnomad NFE
AF:
0.354
Gnomad OTH
AF:
0.445
GnomAD4 exome
AF:
0.358
AC:
408948
AN:
1141688
Hom.:
79164
Cov.:
17
AF XY:
0.358
AC XY:
201560
AN XY:
562730
show subpopulations
Gnomad4 AFR exome
AF:
0.715
Gnomad4 AMR exome
AF:
0.348
Gnomad4 ASJ exome
AF:
0.356
Gnomad4 EAS exome
AF:
0.499
Gnomad4 SAS exome
AF:
0.344
Gnomad4 FIN exome
AF:
0.392
Gnomad4 NFE exome
AF:
0.341
Gnomad4 OTH exome
AF:
0.387
GnomAD4 genome
AF:
0.462
AC:
69900
AN:
151170
Hom.:
18051
Cov.:
28
AF XY:
0.461
AC XY:
34026
AN XY:
73788
show subpopulations
Gnomad4 AFR
AF:
0.705
Gnomad4 AMR
AF:
0.378
Gnomad4 ASJ
AF:
0.355
Gnomad4 EAS
AF:
0.516
Gnomad4 SAS
AF:
0.365
Gnomad4 FIN
AF:
0.405
Gnomad4 NFE
AF:
0.354
Gnomad4 OTH
AF:
0.447
Alfa
AF:
0.381
Hom.:
5470
Bravo
AF:
0.469
Asia WGS
AF:
0.508
AC:
1767
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
16
DANN
Benign
0.83

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: rs11881477; hg19: chr19-39948779; API