rs2066847

chr16-50729867-GC-Gchr16-50729867-GC-GCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PVS1_ModeratePM2_SupportingBP6

The NM_001370466(NOD2):c.2938del(p.Glu981LysfsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

NOD2
NM_001370466 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.98

Links

NOD2 (HGNC:5331):

CYLD-AS1 (HGNC:55352):

LOC124903774 (HGNC:):

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PVS1

Loss of function variant, product does not undergo nonsense mediated mRNA decay. Fraction of 0.0348 CDS is truncated, and there are 0 pathogenic variants in the truncated region.

PM2

Very rare variant; Number of alleles below threshold, Median coverage is 32.

BP6

Variant 16:50729867-GC>G is Benign according to our data. Variant chr16-50729867-GC-G is described in Lovd as [Benign]. Variant chr16-50729867-GC-G is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOD2	NM_001370466.1 linkuse as main transcript	c.2938del	p.Glu981LysfsTer18	frameshift_variant	11/12	ENST00000647318.2
LOC124903774	XR_007065198.1 linkuse as main transcript	n.173del		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOD2	ENST00000647318.2 linkuse as main transcript	c.2938del	p.Glu981LysfsTer18	frameshift_variant	11/12		NM_001370466.1	P1	Q9HC29-2
CYLD-AS1	ENST00000563315.2 linkuse as main transcript	n.1099del		non_coding_transcript_exon_variant	4/6	5

Frequencies

GnomAD3 genomes

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.