rs12035802

Variant names:

• chr1-24162788-T-C
• rs12035802
• NM_170743.4:c.368-1104A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-24162788-T-C
• chr1-24162788-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_170743.4(IFNLR1):​c.368-1104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 12)
  • Failed GnomAD Quality Control
• Consequence: IFNLR1 NM_170743.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNLR1	NM_170743.4	c.368-1104A>G		intron_variant	Intron 3 of 6	ENST00000327535.6	NP_734464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNLR1	ENST00000327535.6	c.368-1104A>G		intron_variant	Intron 3 of 6	1	NM_170743.4	ENSP00000327824.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 70780 Hom.: 0 Cov.: 12

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 70780 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 33840

African (AFR) AF: 0.00 AC: 0 AN: 18088

American (AMR) AF: 0.00 AC: 0 AN: 6268

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1674

East Asian (EAS) AF: 0.00 AC: 0 AN: 3680

South Asian (SAS) AF: 0.00 AC: 0 AN: 2038

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4180

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 130

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 33316

Other (OTH) AF: 0.00 AC: 0 AN: 902

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.45
PhyloP100		-1.6

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

Other links and lift over

dbSNP: rs12035802; hg19: chr1-24489278;