Variant chr21-33403138-T-C 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_001329128.2(IFNGR2):c.-406T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 147,368 control chromosomes in the GnomAD database, including 5,871 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 5868 hom., cov: 27)

Exomes 𝑓: 0.099 ( 3 hom. )

Consequence

IFNGR2
NM_001329128.2 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.194

Variant links:

Genes affected

IFNGR2 (HGNC:):

IFNGR2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 21-33403138-T-C is Benign according to our data. Variant chr21-33403138-T-C is described in ClinVar as [Benign]. Clinvar id is 1289403.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFNGR2	NM_001329128.2 linkuse as main transcript	c.-406T>C		5_prime_UTR_variant	1/8		NP_001316057.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.244

AC:

35825

AN:

147100

Hom.:

5854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.456

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.296

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.109

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.203

GnomAD4 exome

AF:

0.0989

AC:

AN:

182

Hom.:

Cov.:

AF XY:

0.0820

AC XY:

AN XY:

122

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0921

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.244

AC:

35865

AN:

147186

Hom.:

5868

Cov.:

AF XY:

0.245

AC XY:

17535

AN XY:

71690

show subpopulations

Gnomad4 AFR

AF:

0.456

Gnomad4 AMR

AF:

0.178

Gnomad4 ASJ

AF:

0.129

Gnomad4 EAS

AF:

0.422

Gnomad4 SAS

AF:

0.295

Gnomad4 FIN

AF:

0.195

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.200

Alfa

AF:

0.176

Hom.:

437

Bravo

AF:

0.252

Asia WGS

AF:

0.358

AC:

1193

AN:

3340

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 20, 2021	- -
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

-0.94

CADD

Benign

7.3

DANN

Benign

0.36

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