Variant 1-185301203-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_006469.5(IVNS1ABP):c.896-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00292 in 1,604,110 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 70 hom. )

Consequence

IVNS1ABP
NM_006469.5 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00002476

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.418

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 1-185301203-G-A is Benign according to our data. Variant chr1-185301203-G-A is described in ClinVar as [Benign]. Clinvar id is 783014.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00175 (267/152176) while in subpopulation SAS AF= 0.0278 (134/4818). AF 95% confidence interval is 0.024. There are 2 homozygotes in gnomad4. There are 174 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 267 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
IVNS1ABP	NM_006469.5 linkuse as main transcript	c.896-7C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	ENST00000367498.8
IVNS1ABP	XM_047434070.1 linkuse as main transcript	c.896-7C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
IVNS1ABP	XM_047434096.1 linkuse as main transcript	c.629-7C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
IVNS1ABP	XM_047434109.1 linkuse as main transcript	c.242-7C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IVNS1ABP	ENST00000367498.8 linkuse as main transcript	c.896-7C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_006469.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00174

AC:

265

AN:

152058

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00144

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0276

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00132

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00462

AC:

1151

AN:

249282

Hom.:

AF XY:

0.00611

AC XY:

824

AN XY:

134764

show subpopulations

Gnomad AFR exome

AF:

0.000494

Gnomad AMR exome

AF:

0.00131

Gnomad ASJ exome

AF:

0.000802

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0282

Gnomad FIN exome

AF:

0.000186

Gnomad NFE exome

AF:

0.00178

Gnomad OTH exome

AF:

0.00413

GnomAD4 exome

AF:

0.00304

AC:

4418

AN:

1451934

Hom.:

Cov.:

AF XY:

0.00387

AC XY:

2800

AN XY:

722962

show subpopulations

Gnomad4 AFR exome

AF:

0.000302

Gnomad4 AMR exome

AF:

0.00142

Gnomad4 ASJ exome

AF:

0.00127

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0277

Gnomad4 FIN exome

AF:

0.000375

Gnomad4 NFE exome

AF:

0.00146

Gnomad4 OTH exome

AF:

0.00350

GnomAD4 genome

AF:

0.00175

AC:

267

AN:

152176

Hom.:

Cov.:

AF XY:

0.00234

AC XY:

174

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.000193

Gnomad4 AMR

AF:

0.00144

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0278

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00134

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00144

Hom.:

Bravo

AF:

0.00101

Asia WGS

AF:

0.00808

AC:

AN:

3478

EpiCase

AF:

0.00273

EpiControl

AF:

0.00326

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jul 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

8.5

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000025

dbscSNV1_RF

Benign

0.012

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over