6-12123016-A-T

Position:

• chr6-12123016-A-T

Variant summary

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

The ENST00000379388.7(HIVEP1):​c.3221A>T​(p.Asn1074Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N1074S) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HIVEP1 ENST00000379388.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

Genes affected

HIVEP1 (HGNC:4920): (HIVEP zinc finger 1) This gene encodes a transcription factor belonging to the ZAS family, members of which are large proteins that contain a ZAS domain - a modular protein structure consisting of a pair of C2H2 zinc fingers with an acidic-rich region and a serine/threonine-rich sequence. These proteins bind specifically to the DNA sequence motif, GGGACTTTCC, found in the enhancer elements of several viral promoters, including human immunodeficiency virus (HIV), and to related sequences found in the enhancer elements of a number of cellular promoters. This protein binds to this sequence motif, suggesting a role in the transcriptional regulation of both viral and cellular genes. [provided by RefSeq, Oct 2011]

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=0.0858444).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HIVEP1	NM_002114.4	c.3221A>T	p.Asn1074Ile	missense_variant	4/9	ENST00000379388.7	NP_002105.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HIVEP1	ENST00000379388.7	c.3221A>T	p.Asn1074Ile	missense_variant	4/9	1	NM_002114.4	ENSP00000368698	P2
HIVEP1	ENST00000541134.5	c.3221A>T	p.Asn1074Ile	missense_variant	4/9	5		ENSP00000445617	A2
HIVEP1	ENST00000627968.2	c.-3083A>T		5_prime_UTR_variant	4/8	5		ENSP00000486543
HIVEP1	ENST00000442081.6	c.166+3082A>T		intron_variant		3		ENSP00000409078

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 39

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.93
Eigen	Benign	-0.65
Eigen_PC	Benign	-0.74
FATHMM_MKL	Benign	0.26	N
LIST_S2	Benign	0.64	T;.
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.086	T;T
MetaSVM	Benign	-1.0	T
MutationTaster	Benign	1.0	P
PrimateAI	Benign	0.25	T
PROVEAN	Uncertain	-3.5	.;D
REVEL	Benign	0.032
Sift	Uncertain	0.019	.;D
Sift4G	Uncertain	0.043	D;D
Vest4		0.30
MutPred		0.31		Gain of methylation at K1072 (P = 0.0483);Gain of methylation at K1072 (P = 0.0483);
MVP		0.13
MPC		0.17
ClinPred		0.23	T
GERP RS		-0.52
gMVP		0.22

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: rs2228220; hg19: chr6-12123249;