NM_002171.2:c.*100C>T

Variant names:

• chr9-21206428-G-A
• rs12555631
• NM_002171.2:c.*100C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002171.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNA10	NM_002171.2	MANE Select	c.*100C>T		3_prime_UTR	Exon 1 of 1	NP_002162.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNA10	ENST00000357374.2	TSL:6 MANE Select	c.*100C>T		3_prime_UTR	Exon 1 of 1	ENSP00000369566.1

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

African (AFR) AF: 0.206 AC: 6290 AN: 30460

American (AMR) AF: 0.279 AC: 9473 AN: 33952

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 4548 AN: 24082

East Asian (EAS) AF: 0.429 AC: 16935 AN: 39442

South Asian (SAS) AF: 0.118 AC: 9317 AN: 78700

European-Finnish (FIN) AF: 0.186 AC: 9760 AN: 52542

Middle Eastern (MID) AF: 0.139 AC: 547 AN: 3938

European-Non Finnish (NFE) AF: 0.164 AC: 179050 AN: 1090740

Other (OTH) AF: 0.179 AC: 10382 AN: 58130

GnomAD4 genome AF: 0.196 AC: 29831 AN: 151864 Hom.: 3237 Cov.: 32 AF XY: 0.197 AC XY: 14657 AN XY: 74246

African (AFR) AF: 0.204 AC: 8413 AN: 41316

American (AMR) AF: 0.246 AC: 3760 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2129 AN: 5170

South Asian (SAS) AF: 0.120 AC: 579 AN: 4814

European-Finnish (FIN) AF: 0.196 AC: 2073 AN: 10556

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11595 AN: 67970

Other (OTH) AF: 0.194 AC: 409 AN: 2106

Alfa AF: 0.0991 Hom.: 161

Bravo AF: 0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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