1-185296017-G-A

Variant names:

• chr1-185296017-G-A
• rs10798004
• ENST00000718429.1:c.*2018C>T

Variant summary

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

The ENST00000718429.1(IVNS1ABP):​c.*2018C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,504 control chromosomes in the GnomAD database, including 21,824 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 0.52 (21824 hom., cov: 30)
• Consequence: IVNS1ABP ENST00000718429.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 5 publications found

Genes affected

IVNS1ABP (HGNC:16951): (influenza virus NS1A binding protein) Involved in RNA splicing; negative regulation of protein ubiquitination; and response to virus. Located in cytosol. Implicated in immunodeficiency 70. [provided by Alliance of Genome Resources, Apr 2022]

IVNS1ABP Gene-Disease associations (from GenCC):

• immunodeficiency 70

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718429.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IVNS1ABP	ENST00000718429.1		c.*2018C>T		3_prime_UTR	Exon 15 of 15	ENSP00000520813.1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78558 AN: 151398 Hom.: 21790 Cov.: 30

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.519 AC: 78645 AN: 151504 Hom.: 21824 Cov.: 30 AF XY: 0.518 AC XY: 38282 AN XY: 73970

African (AFR) AF: 0.732 AC: 30293 AN: 41388

American (AMR) AF: 0.414 AC: 6289 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1318 AN: 3462

East Asian (EAS) AF: 0.440 AC: 2265 AN: 5146

South Asian (SAS) AF: 0.516 AC: 2483 AN: 4808

European-Finnish (FIN) AF: 0.444 AC: 4620 AN: 10394

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29875 AN: 67818

Other (OTH) AF: 0.467 AC: 981 AN: 2102

Alfa AF: 0.464 Hom.: 43920

Bravo AF: 0.524

Asia WGS AF: 0.437 AC: 1515 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.17
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs10798004; hg19: chr1-185265149;