dbSNP rs11249006: IFNLR1:c.*1146C>T (chr1-24155984-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.*1146C>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 0.305 in 151,946 control chromosomes in the GnomAD database, including 7,687 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 0.31 ( 7685 hom., cov: 32)

Exomes 𝑓: 0.39 ( 2 hom. )

Consequence

IFNLR1
NM_170743.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.306

Publications

14 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 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.*1146C>T	3_prime_UTR	Exon 7 of 7	NP_734464.1
IFNLR1	NM_173064.3		c.*1146C>T	3_prime_UTR	Exon 7 of 7	NP_775087.1
IFNLR1	NM_173065.3		c.*1843C>T	3_prime_UTR	Exon 6 of 6	NP_775088.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IFNLR1	ENST00000327535.6	TSL:1 MANE Select	c.*1146C>T	3_prime_UTR	Exon 7 of 7	ENSP00000327824.1
IFNLR1	ENST00000923176.1		c.*1146C>T	3_prime_UTR	Exon 5 of 5	ENSP00000593235.1
IFNLR1	ENST00000873466.1		c.*1146C>T	3_prime_UTR	Exon 5 of 5	ENSP00000543525.1

Frequencies

GnomAD3 genomes

AF:

0.305

AC:

46367

AN:

151810

Hom.:

7677

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.681

Gnomad SAS

AF:

0.395

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.326

Gnomad OTH

AF:

0.289

GnomAD4 exome

AF:

0.389

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

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:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.429

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.305

AC:

46410

AN:

151928

Hom.:

7685

Cov.:

AF XY:

0.306

AC XY:

22723

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.220

AC:

9117

AN:

41440

American (AMR)

AF:

0.327

AC:

4990

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

1027

AN:

3468

East Asian (EAS)

AF:

0.680

AC:

3494

AN:

5138

South Asian (SAS)

AF:

0.395

AC:

1903

AN:

4820

European-Finnish (FIN)

AF:

0.261

AC:

2753

AN:

10558

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.326

AC:

22127

AN:

67934

Other (OTH)

AF:

0.288

AC:

606

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1607

3213

4820

6426

8033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.313

Hom.:

8172

Bravo

AF:

0.308

Asia WGS

AF:

0.496

AC:

1725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.5

(source)

DANN

Benign

0.46

PhyloP100

0.31

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