NM_001098522.2:c.-392C>T

Variant names:

• chr11-20363846-C-T
• rs2064660878
• NM_001098522.2:c.-392C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Moderate BP6_Moderate

The NM_001098522.2(HTATIP2):​c.-392C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000156 in 1,092,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.000016 (0 hom.)
• Consequence: HTATIP2 NM_001098522.2 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.93
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07304293).
• BP6: Variant 11-20363846-C-T is Benign according to our data. Variant chr11-20363846-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2597340.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098522.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTATIP2	NM_001098522.2	MANE Select	c.-392C>T		5_prime_UTR	Exon 1 of 5	NP_001091992.1	Q9BUP3-1
	HTATIP2	NM_001098520.2		c.35C>T	p.Ala12Val	missense	Exon 1 of 6	NP_001091990.1	Q9BUP3-3
	HTATIP2	NM_001098523.2		c.-392C>T		5_prime_UTR	Exon 1 of 2	NP_001091993.1	Q9BUP3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTATIP2	ENST00000451739.7	TSL:1 MANE Select	c.-392C>T		5_prime_UTR	Exon 1 of 5	ENSP00000394259.2	Q9BUP3-1
	HTATIP2	ENST00000419348.6	TSL:2	c.35C>T	p.Ala12Val	missense	Exon 1 of 6	ENSP00000392985.2	Q9BUP3-3
	HTATIP2	ENST00000421577.6	TSL:2	c.-2+97C>T		intron	N/A	ENSP00000397752.2	Q9BUP3-1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000156 AC: 17 AN: 1092750 Hom.: 0 Cov.: 30 AF XY: 0.0000213 AC XY: 11 AN XY: 517360

African (AFR) AF: 0.00 AC: 0 AN: 22998

American (AMR) AF: 0.00 AC: 0 AN: 8442

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14386

East Asian (EAS) AF: 0.00 AC: 0 AN: 26614

South Asian (SAS) AF: 0.00 AC: 0 AN: 20204

European-Finnish (FIN) AF: 0.0000335 AC: 1 AN: 29824

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3336

European-Non Finnish (NFE) AF: 0.0000162 AC: 15 AN: 923094

Other (OTH) AF: 0.0000228 AC: 1 AN: 43852

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	4.0
DANN	Benign	0.93
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0077	N
LIST_S2	Benign	0.31	T
M_CAP	Benign	0.034	D
MetaRNN	Benign	0.073	T
MetaSVM	Benign	-0.97	T
PhyloP100		-1.9
PrimateAI	Uncertain	0.74	T
PROVEAN	Benign	0.31	N
REVEL	Benign	0.017
Sift	Benign	0.32	T
Sift4G	Benign	0.54	T
Polyphen		0.0	B
Vest4		0.31
MVP		0.095
MPC		0.66
ClinPred		0.23	T
GERP RS		-5.1
PromoterAI		-0.0046	Neutral
gMVP		0.34
Mutation Taster		=296/4	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2064660878; hg19: chr11-20385392;