Variant chr14-104719329-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022489.4(INF2):c.*536G>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 0.471 in 153,774 control chromosomes in the GnomAD database, including 18,548 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 18293 hom., cov: 33)

Exomes 𝑓: 0.53 ( 255 hom. )

Consequence

INF2
NM_022489.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.92

Variant links:

Genes affected

INF2 (HGNC:23791): (inverted formin 2) This gene represents a member of the formin family of proteins. It is considered a diaphanous formin due to the presence of a diaphanous inhibitory domain located at the N-terminus of the encoded protein. Studies of a similar mouse protein indicate that the protein encoded by this locus may function in polymerization and depolymerization of actin filaments. Mutations at this locus have been associated with focal segmental glomerulosclerosis 5.[provided by RefSeq, Aug 2010]

INF2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 14-104719329-G-T is Benign according to our data. Variant chr14-104719329-G-T is described in ClinVar as [Benign]. Clinvar id is 312721.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-104719329-G-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INF2	NM_022489.4 linkuse as main transcript	c.*536G>T		3_prime_UTR_variant	23/23	ENST00000392634.9
INF2	NM_001031714.4 linkuse as main transcript	c.*506G>T		3_prime_UTR_variant	22/22

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INF2	ENST00000392634.9 linkuse as main transcript	c.*536G>T		3_prime_UTR_variant	23/23	5	NM_022489.4	P4	Q27J81-1

Frequencies

GnomAD3 genomes

AF:

0.471

AC:

71495

AN:

151892

Hom.:

18290

Cov.:

show subpopulations

Gnomad AFR

AF:

0.289

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.588

Gnomad ASJ

AF:

0.532

Gnomad EAS

AF:

0.890

Gnomad SAS

AF:

0.564

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.516

GnomAD4 exome

AF:

0.527

AC:

930

AN:

1764

Hom.:

255

Cov.:

AF XY:

0.509

AC XY:

466

AN XY:

916

show subpopulations

Gnomad4 AFR exome

AF:

0.125

Gnomad4 AMR exome

AF:

0.579

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.917

Gnomad4 SAS exome

AF:

0.564

Gnomad4 FIN exome

AF:

0.438

Gnomad4 NFE exome

AF:

0.519

Gnomad4 OTH exome

AF:

0.510

GnomAD4 genome

AF:

0.470

AC:

71520

AN:

152010

Hom.:

18293

Cov.:

AF XY:

0.476

AC XY:

35348

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.289

Gnomad4 AMR

AF:

0.588

Gnomad4 ASJ

AF:

0.532

Gnomad4 EAS

AF:

0.890

Gnomad4 SAS

AF:

0.564

Gnomad4 FIN

AF:

0.494

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.518

Alfa

AF:

0.477

Hom.:

8670

Bravo

AF:

0.471

Asia WGS

AF:

0.695

AC:

2412

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jul 15, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 89% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 83. Only high quality variants are reported. -

Focal segmental glomerulosclerosis 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.55

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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