Genetic Variant ENSG00000198358:n.792G>C (chr1-160945127-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000356006.3(ENSG00000198358):n.792G>C variant causes a non coding transcript exon 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

ENSG00000198358
ENST00000356006.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.889

Publications

6 publications found

Variant links:

Genes affected

ENSG00000198358 (HGNC:):

ENSG00000198358 links:

ITLN2 (HGNC:20599): (intelectin 2) Predicted to enable oligosaccharide binding activity. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ITLN2 links:

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ACMG classification

Classification was made for transcript

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=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ITLN2	NM_080878.3 link	c.*13C>G	3_prime_UTR_variant	Exon 8 of 8	ENST00000368029.4	NP_543154.1	Q8WWU7-1
LOC101928372	NR_110695.1 link	n.792G>C	non_coding_transcript_exon_variant	Exon 5 of 6
ITLN2	XM_024453321.2 link	c.*13C>G	3_prime_UTR_variant	Exon 8 of 8		XP_024309089.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000198358	ENST00000356006.3 link	n.792G>C	non_coding_transcript_exon_variant	Exon 5 of 6	1
ITLN2	ENST00000368029.4 link	c.*13C>G	3_prime_UTR_variant	Exon 8 of 8	1	NM_080878.3	ENSP00000357008.3	Q8WWU7-1
ITLN2	ENST00000494442.1 link	n.851C>G	non_coding_transcript_exon_variant	Exon 4 of 4	3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

198952

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1410544

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

701430

African (AFR)

AF:

0.00

AC:

AN:

29700

American (AMR)

AF:

0.00

AC:

AN:

29974

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24352

East Asian (EAS)

AF:

0.00

AC:

AN:

36108

South Asian (SAS)

AF:

0.00

AC:

AN:

77020

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52824

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5632

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1096608

Other (OTH)

AF:

0.00

AC:

AN:

58326

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.10

(source)

DANN

Benign

0.48

PhyloP100

-0.89

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

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over