rs661225

Variant names:

• chr1-41844494-G-A
• rs661225
• NM_024503.5:c.-801+73919C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-41844494-G-A
• chr1-41844494-G-T

Variant summary

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

The NM_024503.5(HIVEP3):​c.-801+73919C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,056 control chromosomes in the GnomAD database, including 30,903 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 0.62 (30903 hom., cov: 32)
• Consequence: HIVEP3 NM_024503.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIVEP3	NM_024503.5	c.-801+73919C>T		intron_variant	Intron 1 of 8	ENST00000372583.6	NP_078779.2
HIVEP3	NM_001127714.3	c.-721+73919C>T		intron_variant	Intron 1 of 7		NP_001121186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIVEP3	ENST00000372583.6	c.-801+73919C>T		intron_variant	Intron 1 of 8	1	NM_024503.5	ENSP00000361664.1
HIVEP3	ENST00000372584.5	c.-721+73919C>T		intron_variant	Intron 1 of 7	1		ENSP00000361665.1

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94569 AN: 151938 Hom.: 30870 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.623 AC: 94661 AN: 152056 Hom.: 30903 Cov.: 32 AF XY: 0.613 AC XY: 45583 AN XY: 74308

African (AFR) AF: 0.807 AC: 33486 AN: 41482

American (AMR) AF: 0.560 AC: 8540 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2125 AN: 3470

East Asian (EAS) AF: 0.193 AC: 996 AN: 5170

South Asian (SAS) AF: 0.440 AC: 2118 AN: 4818

European-Finnish (FIN) AF: 0.566 AC: 5979 AN: 10568

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39517 AN: 67972

Other (OTH) AF: 0.619 AC: 1309 AN: 2114

Alfa AF: 0.606 Hom.: 4982

Bravo AF: 0.632

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.75
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs661225; hg19: chr1-42310165;