11-20383113-A-G

Variant names:

• chr11-20383113-A-G
• NM_001098522.2:c.637A>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001098522.2(HTATIP2):​c.637A>G​(p.Asn213Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,864 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: HTATIP2 NM_001098522.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.38

Genes affected

HTATIP2 (HGNC:16637): (HIV-1 Tat interactive protein 2) Enables protein serine/threonine kinase activity. Involved in import into nucleus and regulation of angiogenesis. Acts upstream of or within positive regulation of programmed cell death; positive regulation of transcription by RNA polymerase II; and protein autophosphorylation. Located in cytosol and nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.36844838).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTATIP2	NM_001098522.2	c.637A>G	p.Asn213Asp	missense_variant	Exon 5 of 5	ENST00000451739.7	NP_001091992.1
HTATIP2	NM_001098520.2	c.739A>G	p.Asn247Asp	missense_variant	Exon 6 of 6		NP_001091990.1
HTATIP2	NM_001098521.2	c.637A>G	p.Asn213Asp	missense_variant	Exon 6 of 6		NP_001091991.1
HTATIP2	NM_006410.5	c.637A>G	p.Asn213Asp	missense_variant	Exon 6 of 6		NP_006401.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTATIP2	ENST00000451739.7	c.637A>G	p.Asn213Asp	missense_variant	Exon 5 of 5	1	NM_001098522.2	ENSP00000394259.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461864 Hom.: 0 Cov.: 38 AF XY: 0.00000138 AC XY: 1 AN XY: 727224

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Benign	-0.090	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.22	T;T;.;T;.
Eigen	Benign	-0.039
Eigen_PC	Benign	-0.022
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.81	.;.;T;T;T
M_CAP	Benign	0.013	T
MetaRNN	Benign	0.37	T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.5	L;L;.;L;.
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	-1.7	N;N;N;N;N
REVEL	Benign	0.21
Sift	Benign	0.12	T;T;T;T;T
Sift4G	Benign	0.64	T;T;D;T;T
Polyphen		0.71	P;P;P;P;.
Vest4		0.51
MutPred		0.69		Loss of MoRF binding (P = 0.0432);Loss of MoRF binding (P = 0.0432);.;Loss of MoRF binding (P = 0.0432);.;
MVP		0.43
MPC		0.90
ClinPred		0.79	D
GERP RS		2.5
Varity_R		0.38
gMVP		0.86

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-20404659;