rs616366

Variant names:

• chr1-41812110-T-A
• rs616366
• NM_024503.5:c.-801+106303A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-41812110-T-A
• chr1-41812110-T-C
• chr1-41812110-T-G

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+106303A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,020 control chromosomes in the GnomAD database, including 11,908 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 0.37 (11908 hom., cov: 31)
• Consequence: HIVEP3 NM_024503.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIVEP3	NM_024503.5	c.-801+106303A>T		intron_variant	Intron 1 of 8	ENST00000372583.6	NP_078779.2
HIVEP3	NM_001127714.3	c.-721+106303A>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+106303A>T		intron_variant	Intron 1 of 8	1	NM_024503.5	ENSP00000361664.1
HIVEP3	ENST00000372584.5	c.-721+106303A>T		intron_variant	Intron 1 of 7	1		ENSP00000361665.1

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56940 AN: 151904 Hom.: 11905 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.375 AC: 56976 AN: 152020 Hom.: 11908 Cov.: 31 AF XY: 0.384 AC XY: 28498 AN XY: 74300

African (AFR) AF: 0.213 AC: 8848 AN: 41482

American (AMR) AF: 0.448 AC: 6844 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3468

East Asian (EAS) AF: 0.799 AC: 4131 AN: 5170

South Asian (SAS) AF: 0.553 AC: 2665 AN: 4816

European-Finnish (FIN) AF: 0.408 AC: 4307 AN: 10546

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27700 AN: 67958

Other (OTH) AF: 0.383 AC: 806 AN: 2106

Alfa AF: 0.384 Hom.: 1440

Bravo AF: 0.369

Asia WGS AF: 0.640 AC: 2222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.36
DANN	Benign	0.43
PhyloP100		-1.2
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: rs616366; hg19: chr1-42277781;