9-21207038-A-T

Position:

• chr9-21207038-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002171.2(IFNA10):​c.60T>A​(p.Cys20*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,508,488 control chromosomes in the GnomAD database, including 47,160 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 0.28 (6515 hom., cov: 31)
  • Exomes 𝑓: 0.21 (40645 hom.)
• Consequence: IFNA10 NM_002171.2 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFNA10	NM_002171.2	c.60T>A	p.Cys20*	stop_gained	1/1	ENST00000357374.2	NP_002162.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNA10	ENST00000357374.2	c.60T>A	p.Cys20*	stop_gained	1/1	6	NM_002171.2	ENSP00000369566.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42027 AN: 150904 Hom.: 6506 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.269

GnomAD3 exomes AF: 0.216 AC: 49259 AN: 227702 Hom.: 7756 AF XY: 0.203 AC XY: 25080 AN XY: 123438

Gnomad AFR exome AF: 0.330

Gnomad AMR exome AF: 0.304

Gnomad ASJ exome AF: 0.160

Gnomad EAS exome AF: 0.507

Gnomad SAS exome AF: 0.155

Gnomad FIN exome AF: 0.183

Gnomad NFE exome AF: 0.157

Gnomad OTH exome AF: 0.194

GnomAD4 exome AF: 0.206 AC: 279840 AN: 1357462 Hom.: 40645 Cov.: 33 AF XY: 0.204 AC XY: 138193 AN XY: 676962

Gnomad4 AFR exome AF: 0.356

Gnomad4 AMR exome AF: 0.334

Gnomad4 ASJ exome AF: 0.211

Gnomad4 EAS exome AF: 0.541

Gnomad4 SAS exome AF: 0.176

Gnomad4 FIN exome AF: 0.205

Gnomad4 NFE exome AF: 0.186

Gnomad4 OTH exome AF: 0.220

GnomAD4 genome AF: 0.279 AC: 42081 AN: 151026 Hom.: 6515 Cov.: 31 AF XY: 0.278 AC XY: 20495 AN XY: 73774

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.268

Alfa AF: 0.168 Hom.: 715

Bravo AF: 0.296

ExAC AF: 0.225 AC: 27227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Uncertain	-0.060
CADD	Pathogenic	36
DANN	Uncertain	0.99
Eigen	Benign	-0.33
Eigen_PC	Benign	-0.71
FATHMM_MKL	Benign	0.0023	N
Vest4		0.023
GERP RS		-0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10119910; hg19: chr9-21207037; COSMIC: COSV53330839; COSMIC: COSV53330839;