rs12555631

Positions:

• chr9-21206428-G-A
• chr9-21206428-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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]

ACMG classification

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	UniProt
IFNA10	NM_002171.2	c.*100C>T		3_prime_UTR_variant	1/1	ENST00000357374.2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29806 AN: 151746 Hom.: 3236 Cov.: 32

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.: 28 AF XY: 0.172 AC XY: 120688 AN XY: 701482

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.: 32 AF XY: 0.197 AC XY: 14657 AN XY: 74246

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

Other links and lift over

dbSNP: rs12555631; hg19: chr9-21206427; COSMIC: COSV53332587; COSMIC: COSV53332587;