NM_001014336.2:c.166-95G>T

Variant names:

• chr12-122172836-C-A
• rs7977932
• NM_001014336.2:c.166-95G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001014336.2(IL31):​c.166-95G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IL31 NM_001014336.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 23 publications found

Genes affected

IL31 (HGNC:19372): (interleukin 31) IL31, which is made principally by activated Th2-type T cells, interacts with a heterodimeric receptor consisting of IL31RA (MIM 609510) and OSMR (MIM 601743) that is constitutively expressed on epithelial cells and keratinocytes. IL31 may be involved in the promotion of allergic skin disorders and in regulating other allergic diseases, such as asthma (Dillon et al., 2004 [PubMed 15184896]).[supplied by OMIM, Mar 2008]

LRRC43 (HGNC:28562): (leucine rich repeat containing 43)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001014336.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL31	NM_001014336.2	MANE Select	c.166-95G>T		intron	N/A	NP_001014358.1
	LRRC43	NM_152759.5		c.-406+5054C>A		intron	N/A	NP_689972.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL31	ENST00000377035.2	TSL:1 MANE Select	c.166-95G>T		intron	N/A	ENSP00000366234.1
	LRRC43	ENST00000537729.5	TSL:5	c.-406+5054C>A		intron	N/A	ENSP00000438751.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 792436 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 402710

African (AFR) AF: 0.00 AC: 0 AN: 19180

American (AMR) AF: 0.00 AC: 0 AN: 24968

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17046

East Asian (EAS) AF: 0.00 AC: 0 AN: 32852

South Asian (SAS) AF: 0.00 AC: 0 AN: 54664

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44998

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2666

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 558890

Other (OTH) AF: 0.00 AC: 0 AN: 37172

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.14
PhyloP100		0.066

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: rs7977932; hg19: chr12-122657383;