rs1447318632

Variant names:

• chrX-136497803-C-G
• rs1447318632
• NM_014500.5:c.119C>G

Your query was ambiguous. Multiple possible variants found:

• chrX-136497803-C-G
• chrX-136497803-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_014500.5(HTATSF1):​c.119C>G​(p.Ser40Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000089 in 112,398 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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 0.0000089 (0 hom., 0 hem., cov: 24)
• Consequence: HTATSF1 NM_014500.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.86

Genes affected

HTATSF1 (HGNC:5276): (HIV-1 Tat specific factor 1) The protein encoded by this gene functions as a cofactor for the stimulation of transcriptional elongation by HIV-1 Tat, which binds to the HIV-1 promoter through Tat-TAR interaction. This protein may also serve as a dual-function factor to couple transcription and splicing and to facilitate their reciprocal activation. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.24827045).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTATSF1	NM_014500.5	c.119C>G	p.Ser40Cys	missense_variant	Exon 1 of 9	ENST00000218364.5	NP_055315.2
HTATSF1	NM_001163280.2	c.119C>G	p.Ser40Cys	missense_variant	Exon 2 of 10		NP_001156752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTATSF1	ENST00000218364.5	c.119C>G	p.Ser40Cys	missense_variant	Exon 1 of 9	1	NM_014500.5	ENSP00000218364.4
HTATSF1	ENST00000535601.5	c.119C>G	p.Ser40Cys	missense_variant	Exon 2 of 10	1		ENSP00000442699.1
HTATSF1	ENST00000448450.5	c.119C>G	p.Ser40Cys	missense_variant	Exon 2 of 6	5		ENSP00000411381.1
HTATSF1	ENST00000425695.5	c.119C>G	p.Ser40Cys	missense_variant	Exon 2 of 6	3		ENSP00000412420.1

Frequencies

GnomAD3 genomes AF: 0.00000890 AC: 1 AN: 112398 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 AN XY: 34544

Gnomad AFR AF: 0.0000323

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 29

GnomAD4 genome AF: 0.00000890 AC: 1 AN: 112398 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 AN XY: 34544

Gnomad4 AFR AF: 0.0000323

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.18	T;T;T;T
FATHMM_MKL	Benign	0.43	N
LIST_S2	Benign	0.70	T;T;T;.
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.25	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.5	M;.;.;M
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-1.9	N;N;N;N
REVEL	Benign	0.10
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Uncertain	0.026	D;T;T;D
Polyphen		1.0	D;.;.;D
Vest4		0.23
MutPred		0.20		Loss of glycosylation at S40 (P = 0.0076);Loss of glycosylation at S40 (P = 0.0076);Loss of glycosylation at S40 (P = 0.0076);Loss of glycosylation at S40 (P = 0.0076);
MVP		0.44
MPC		1.2
ClinPred		0.95	D
GERP RS		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Varity_R		0.33
gMVP		0.49

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

Other links and lift over

dbSNP: rs1447318632; hg19: chrX-135579962;