rs1208517

chr1-185303351-C-T

Variant summary

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

The NM_006469.5(IVNS1ABP):c.766-1788G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,084 control chromosomes in the GnomAD database, including 1,111 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 0.10 (1111 hom., cov: 32)
• Consequence: IVNS1ABP NM_006469.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IVNS1ABP	NM_006469.5	c.766-1788G>A		intron_variant		ENST00000367498.8
IVNS1ABP	XM_047434070.1	c.766-1788G>A		intron_variant
IVNS1ABP	XM_047434096.1	c.499-1788G>A		intron_variant
IVNS1ABP	XM_047434109.1	c.112-1788G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IVNS1ABP	ENST00000367498.8	c.766-1788G>A		intron_variant		1	NM_006469.5	P1
IVNS1ABP	ENST00000480769.5	n.966-1788G>A		intron_variant, non_coding_transcript_variant		1
IVNS1ABP	ENST00000459929.5	n.1474-1788G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15793 AN: 151966 Hom.: 1112 Cov.: 32

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.104 AC: 15783 AN: 152084 Hom.: 1111 Cov.: 32 AF XY: 0.102 AC XY: 7556 AN XY: 74348

Gnomad4 AFR AF: 0.0288

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0435

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.107

Alfa AF: 0.139 Hom.: 1574

Bravo AF: 0.0983

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.3
Dann	Benign	0.63

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: rs1208517; hg19: chr1-185272483; COSMIC: COSV62249900; COSMIC: COSV62249900;