rs7554964

chr1-41912558-T-Cchr1-41912558-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024503.5(HIVEP3):c.-801+5855A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,052 control chromosomes in the GnomAD database, including 24,433 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 0.56 (24433 hom., cov: 32)
• Consequence: HIVEP3 NM_024503.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

Genes affected

HIVEP3 (HGNC:13561): (HIVEP zinc finger 3) This gene encodes a member of the human immunodeficiency virus type 1 enhancer-binding protein family. Members of this protein family contain multiple zinc finger and acid-rich (ZAS) domains and serine-threonine rich regions. This protein acts as a transcription factor and is able to regulate nuclear factor kappaB-mediated transcription by binding the kappaB motif in target genes. This protein also binds the recombination signal sequence that flanks the V, D, and J regions of immunoglobulin and T-cell receptors. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIVEP3	NM_024503.5	c.-801+5855A>G		intron_variant		ENST00000372583.6
HIVEP3	NM_001127714.3	c.-721+5855A>G		intron_variant
HIVEP3	NR_038260.2	n.510+5855A>G		intron_variant, non_coding_transcript_variant
HIVEP3	NR_038261.2	n.240+5855A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIVEP3	ENST00000372583.6	c.-801+5855A>G		intron_variant		1	NM_024503.5	P5
HIVEP3	ENST00000372584.5	c.-721+5855A>G		intron_variant		1		A2
HIVEP3	ENST00000489103.5	n.231+5855A>G		intron_variant, non_coding_transcript_variant		1
HIVEP3	ENST00000491442.5	n.257+5855A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85690 AN: 151934 Hom.: 24402 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.564 AC: 85768 AN: 152052 Hom.: 24433 Cov.: 32 AF XY: 0.560 AC XY: 41630 AN XY: 74308

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.543

Alfa AF: 0.564 Hom.: 3034

Bravo AF: 0.560

Asia WGS AF: 0.606 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.58
Dann	Benign	0.42

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: rs7554964; hg19: chr1-42378229;