dbSNP rs10903035: IFNLR1:c.*1680C>T (chr1-24155450-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_170743.4(IFNLR1):c.*1680C>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 0.626 in 152,038 control chromosomes in the GnomAD database, including 30,061 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 0.63 ( 30053 hom., cov: 32)

Exomes 𝑓: 0.60 ( 8 hom. )

Consequence

IFNLR1
NM_170743.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.196

Publications

17 publications found

Variant links:

Genes affected

IFNLR1 (HGNC:18584): (interferon lambda receptor 1) The protein encoded by this gene belongs to the class II cytokine receptor family. This protein forms a receptor complex with interleukine 10 receptor, beta (IL10RB). The receptor complex has been shown to interact with three closely related cytokines, including interleukin 28A (IL28A), interleukin 28B (IL28B), and interleukin 29 (IL29). The expression of all three cytokines can be induced by viral infection. The cells overexpressing this protein have been found to have enhanced responses to IL28A and IL29, but decreased response to IL28B. Three alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

IFNLR1 links:

LOC124903879 (HGNC:):

LOC124903879 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_170743.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IFNLR1	NM_170743.4	MANE Select	c.*1680C>T	3_prime_UTR	Exon 7 of 7	NP_734464.1
IFNLR1	NM_173064.3		c.*1680C>T	3_prime_UTR	Exon 7 of 7	NP_775087.1
IFNLR1	NM_173065.3		c.*2377C>T	3_prime_UTR	Exon 6 of 6	NP_775088.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNLR1	ENST00000327535.6	TSL:1 MANE Select	c.*1680C>T		3_prime_UTR	Exon 7 of 7	ENSP00000327824.1

Frequencies

GnomAD3 genomes

AF:

0.626

AC:

95128

AN:

151890

Hom.:

30040

Cov.:

show subpopulations

Gnomad AFR

AF:

0.560

Gnomad AMI

AF:

0.594

Gnomad AMR

AF:

0.652

Gnomad ASJ

AF:

0.650

Gnomad EAS

AF:

0.467

Gnomad SAS

AF:

0.623

Gnomad FIN

AF:

0.730

Gnomad MID

AF:

0.641

Gnomad NFE

AF:

0.655

Gnomad OTH

AF:

0.649

GnomAD4 exome

AF:

0.600

AC:

AN:

Hom.:

Cov.:

AF XY:

0.450

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.600

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.725

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.626

AC:

95173

AN:

152008

Hom.:

30053

Cov.:

AF XY:

0.629

AC XY:

46758

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.560

AC:

23209

AN:

41460

American (AMR)

AF:

0.651

AC:

9939

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.650

AC:

2258

AN:

3472

East Asian (EAS)

AF:

0.467

AC:

2410

AN:

5162

South Asian (SAS)

AF:

0.622

AC:

2995

AN:

4818

European-Finnish (FIN)

AF:

0.730

AC:

7710

AN:

10558

Middle Eastern (MID)

AF:

0.655

AC:

190

AN:

290

European-Non Finnish (NFE)

AF:

0.655

AC:

44550

AN:

67966

Other (OTH)

AF:

0.650

AC:

1370

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1799

3598

5396

7195

8994

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

782

1564

2346

3128

3910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.646

Hom.:

41147

Bravo

AF:

0.615

Asia WGS

AF:

0.591

AC:

2051

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.98

(source)

DANN

Benign

0.45

PhyloP100

-0.20

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over