rs10113875

Variant names:

• chr9-21207001-C-G
• rs10113875
• NM_002171.2:c.97G>C

Your query was ambiguous. Multiple possible variants found:

• chr9-21207001-C-G
• chr9-21207001-C-A
• chr9-21207001-C-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_002171.2(IFNA10):​c.97G>C​(p.Gly33Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 1,585,982 control chromosomes in the GnomAD database, including 48,179 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.28 (6533 hom., cov: 31)
  • Exomes 𝑓: 0.22 (41646 hom.)
• Consequence: IFNA10 NM_002171.2 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.14
• Publications: 16 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0019498467).
• BP6: Variant 9-21207001-C-G is Benign according to our data. Variant chr9-21207001-C-G is described in ClinVar as Benign. ClinVar VariationId is 768283.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNA10	NM_002171.2	MANE Select	c.97G>C	p.Gly33Arg	missense	Exon 1 of 1	NP_002162.1	P01566

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNA10	ENST00000357374.2	TSL:6 MANE Select	c.97G>C	p.Gly33Arg	missense	Exon 1 of 1	ENSP00000369566.1	P01566

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42125 AN: 151026 Hom.: 6524 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.268

GnomAD2 exomes AF: 0.237 AC: 55705 AN: 235466 AF XY: 0.222

Gnomad AFR exome AF: 0.350

Gnomad AMR exome AF: 0.337

Gnomad ASJ exome AF: 0.184

Gnomad EAS exome AF: 0.518

Gnomad FIN exome AF: 0.194

Gnomad NFE exome AF: 0.177

Gnomad OTH exome AF: 0.212

GnomAD4 exome AF: 0.224 AC: 320795 AN: 1434832 Hom.: 41646 Cov.: 33 AF XY: 0.221 AC XY: 158210 AN XY: 714700

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.368 AC: 11998 AN: 32584

American (AMR) AF: 0.352 AC: 15648 AN: 44422

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 5846 AN: 25734

East Asian (EAS) AF: 0.541 AC: 21412 AN: 39546

South Asian (SAS) AF: 0.185 AC: 15862 AN: 85632

European-Finnish (FIN) AF: 0.207 AC: 11062 AN: 53330

Middle Eastern (MID) AF: 0.209 AC: 1188 AN: 5696

European-Non Finnish (NFE) AF: 0.206 AC: 223823 AN: 1088500

Other (OTH) AF: 0.235 AC: 13956 AN: 59388

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.279 AC: 42180 AN: 151150 Hom.: 6533 Cov.: 31 AF XY: 0.278 AC XY: 20542 AN XY: 73848

African (AFR) AF: 0.376 AC: 15385 AN: 40910

American (AMR) AF: 0.309 AC: 4702 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 830 AN: 3464

East Asian (EAS) AF: 0.510 AC: 2600 AN: 5098

South Asian (SAS) AF: 0.200 AC: 959 AN: 4802

European-Finnish (FIN) AF: 0.213 AC: 2252 AN: 10548

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14665 AN: 67818

Other (OTH) AF: 0.267 AC: 563 AN: 2106

Alfa AF: 0.177 Hom.: 879

Bravo AF: 0.296

ExAC AF: 0.236 AC: 28693

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.83	T
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.011
DANN	Benign	0.60
DEOGEN2	Benign	0.00064	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.0096	N
LIST_S2	Benign	0.12	T
MetaRNN	Benign	0.0019	T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	1.0	L
PhyloP100		-2.1
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.97	N
REVEL	Benign	0.013
Sift	Benign	0.78	T
Sift4G	Benign	0.54	T
Polyphen		0.017	B
Vest4		0.018
MPC		0.13
ClinPred		0.0034	T
GERP RS		-4.7
PromoterAI		0.067	Neutral
Varity_R		0.077
gMVP		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs10113875; hg19: chr9-21207000; COSMIC: COSV53330834; COSMIC: COSV53330834;