rs6682925

Variant names:

• chr1-67165579-C-A
• rs6682925
• ENST00000637002.1:n.-29-2513C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-67165579-C-A
• chr1-67165579-C-G
• chr1-67165579-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000371007.6(C1orf141):​c.-103-34352G>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)
• Consequence: C1orf141 ENST00000371007.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

Genes affected

IL23R (HGNC:19100): (interleukin 23 receptor) The protein encoded by this gene is a subunit of the receptor for IL23A/IL23. This protein pairs with the receptor molecule IL12RB1/IL12Rbeta1, and both are required for IL23A signaling. This protein associates constitutively with Janus kinase 2 (JAK2), and also binds to transcription activator STAT3 in a ligand-dependent manner. [provided by RefSeq, Jul 2008]

C1orf141 (HGNC:32044): (chromosome 1 open reading frame 141)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL23R	XM_011540790.4	c.-29-2513C>A		intron_variant	Intron 1 of 10		XP_011539092.1
IL23R	XM_011540791.4	c.-29-2513C>A		intron_variant	Intron 1 of 10		XP_011539093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL23R	ENST00000637002.1	n.-29-2513C>A		intron_variant	Intron 1 of 10	1		ENSP00000490340.2
C1orf141	ENST00000371007.6	c.-103-34352G>T		intron_variant	Intron 1 of 7	5		ENSP00000360046.1
C1orf141	ENST00000448166.6	c.-103-34352G>T		intron_variant	Intron 1 of 9	5		ENSP00000415519.2
IL23R	ENST00000697222.1	c.-29-2513C>A		intron_variant	Intron 1 of 2			ENSP00000513189.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6682925; hg19: chr1-67631262;