5-32588543-A-T

Variant names:

• chr5-32588543-A-T
• rs17850527
• NM_006713.4:c.31A>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_006713.4(SUB1):​c.31A>T​(p.Ser11Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SUB1 NM_006713.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.08
• Publications: 2 publications found

Genes affected

SUB1 (HGNC:19985): (SUB1 regulator of transcription) Enables identical protein binding activity; single-stranded DNA binding activity; and transcription coactivator activity. Involved in negative regulation of DNA metabolic process and regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of transcription regulator complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.377948).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUB1	NM_006713.4	c.31A>T	p.Ser11Cys	missense_variant	Exon 2 of 5	ENST00000265073.9	NP_006704.3
SUB1	XM_011513944.4	c.31A>T	p.Ser11Cys	missense_variant	Exon 3 of 6		XP_011512246.1
SUB1	XM_047416661.1	c.31A>T	p.Ser11Cys	missense_variant	Exon 3 of 6		XP_047272617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUB1	ENST00000265073.9	c.31A>T	p.Ser11Cys	missense_variant	Exon 2 of 5	1	NM_006713.4	ENSP00000265073.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Uncertain	0.025	T
BayesDel_noAF	Benign	-0.20
CADD	Uncertain	26
DANN	Uncertain	0.98
DEOGEN2	Benign	0.093	T;T;T;T;T;.
Eigen	Pathogenic	0.69
Eigen_PC	Pathogenic	0.69
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.80	.;.;.;.;T;T
M_CAP	Benign	0.037	D
MetaRNN	Benign	0.38	T;T;T;T;T;T
MetaSVM	Uncertain	-0.26	T
MutationAssessor	Benign	1.9	L;L;L;L;L;.
PhyloP100		6.1
PrimateAI	Uncertain	0.79	T
PROVEAN	Benign	-2.0	N;N;N;N;N;D
REVEL	Benign	0.17
Sift	Uncertain	0.0080	D;D;D;D;D;D
Sift4G	Uncertain	0.0040	D;D;D;D;D;D
Polyphen		1.0	D;D;D;D;D;.
Vest4		0.42
MutPred		0.32		Loss of phosphorylation at S11 (P = 5e-04);Loss of phosphorylation at S11 (P = 5e-04);Loss of phosphorylation at S11 (P = 5e-04);Loss of phosphorylation at S11 (P = 5e-04);Loss of phosphorylation at S11 (P = 5e-04);Loss of phosphorylation at S11 (P = 5e-04);
MVP		0.51
MPC		0.071
ClinPred		0.79	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.25
gMVP		0.31
Mutation Taster		=67/33	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17850527; hg19: chr5-32588649;