Variant rs12555631 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002171.2(IFNA10):c.*100C>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 0.177 in 1,563,850 control chromosomes in the GnomAD database, including 27,112 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 0.20 ( 3237 hom., cov: 32)

Exomes 𝑓: 0.17 ( 23875 hom. )

Consequence

IFNA10
NM_002171.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21

Variant links:

Genes affected

IFNA10 (HGNC:5418): (interferon alpha 10) This gene encodes a protein that belongs to the type I interferon family of proteins, and is located in a cluster of alpha interferon genes on chromosome 9. Interferons are small regulatory molecules that function in cell signaling in response to viruses and other pathogens or tumor cells. This gene is intronless and the encoded protein is secreted. [provided by RefSeq, Aug 2013]

IFNA10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFNA10	NM_002171.2 linkuse as main transcript	c.*100C>T		3_prime_UTR_variant	1/1	ENST00000357374.2	NP_002162.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNA10	ENST00000357374.2 linkuse as main transcript	c.*100C>T		3_prime_UTR_variant	1/1		NM_002171.2	ENSP00000369566	P1

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29806

AN:

151746

Hom.:

3236

Cov.:

show subpopulations

Gnomad AFR

AF:

0.204

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.246

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.412

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.196

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.194

GnomAD4 exome

AF:

0.174

AC:

246302

AN:

1411986

Hom.:

23875

Cov.:

AF XY:

0.172

AC XY:

120688

AN XY:

701482

show subpopulations

Gnomad4 AFR exome

AF:

0.206

Gnomad4 AMR exome

AF:

0.279

Gnomad4 ASJ exome

AF:

0.189

Gnomad4 EAS exome

AF:

0.429

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.186

Gnomad4 NFE exome

AF:

0.164

Gnomad4 OTH exome

AF:

0.179

GnomAD4 genome

AF:

0.196

AC:

29831

AN:

151864

Hom.:

3237

Cov.:

AF XY:

0.197

AC XY:

14657

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.204

Gnomad4 AMR

AF:

0.246

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.412

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.196

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.194

Alfa

AF:

0.0943

Hom.:

143

Bravo

AF:

0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.1

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over