chr11-20356578-G-A

Variant names:

• chr11-20356578-G-A
• rs11025523
• ENST00000868110.1:c.-84G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000868110.1(HTATIP2):​c.-84G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,104 control chromosomes in the GnomAD database, including 3,050 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 0.18 (3050 hom., cov: 32)
• Consequence: HTATIP2 ENST00000868110.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 14 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000868110.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTATIP2	ENST00000868110.1		c.-84G>A		5_prime_UTR	Exon 1 of 6	ENSP00000538169.1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27847 AN: 151986 Hom.: 3051 Cov.: 32

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.169

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.183 AC: 27841 AN: 152104 Hom.: 3050 Cov.: 32 AF XY: 0.189 AC XY: 14067 AN XY: 74326

African (AFR) AF: 0.0811 AC: 3367 AN: 41514

American (AMR) AF: 0.118 AC: 1811 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3472

East Asian (EAS) AF: 0.150 AC: 774 AN: 5156

South Asian (SAS) AF: 0.329 AC: 1586 AN: 4816

European-Finnish (FIN) AF: 0.320 AC: 3384 AN: 10560

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.233 AC: 15842 AN: 67990

Other (OTH) AF: 0.168 AC: 354 AN: 2108

Alfa AF: 0.211 Hom.: 13630

Bravo AF: 0.160

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.67
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs11025523; hg19: chr11-20378124;