rs6701920

Positions:

• chr1-160945127-G-A
• chr1-160945127-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080878.3(ITLN2):​c.*13C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00492 in 1,562,772 control chromosomes in the GnomAD database, including 389 homozygotes. 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 0.028 (226 hom., cov: 32)
  • Exomes 𝑓: 0.0024 (163 hom.)
• Consequence: ITLN2 NM_080878.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889

Genes affected

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]

ENSG00000198358 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITLN2	NM_080878.3	c.*13C>T		3_prime_UTR_variant	8/8	ENST00000368029.4	NP_543154.1
ITLN2	XM_024453321.2	c.*13C>T		3_prime_UTR_variant	8/8		XP_024309089.1
LOC101928372	NR_110695.1	n.792G>A		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITLN2	ENST00000368029.4	c.*13C>T		3_prime_UTR_variant	8/8	1	NM_080878.3	ENSP00000357008.3
ENSG00000198358	ENST00000356006.3	n.792G>A		non_coding_transcript_exon_variant	5/6	1
ITLN2	ENST00000494442.1	n.851C>T		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes AF: 0.0278 AC: 4236 AN: 152128 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0108

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.0168

GnomAD3 exomes AF: 0.00713 AC: 1418 AN: 198952 Hom.: 71 AF XY: 0.00513 AC XY: 562 AN XY: 109498

Gnomad AFR exome AF: 0.0991

Gnomad AMR exome AF: 0.00343

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000182

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000225

Gnomad OTH exome AF: 0.00392

GnomAD4 exome AF: 0.00244 AC: 3445 AN: 1410526 Hom.: 163 Cov.: 30 AF XY: 0.00215 AC XY: 1506 AN XY: 701422

Gnomad4 AFR exome AF: 0.0969

Gnomad4 AMR exome AF: 0.00464

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000156

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000830

Gnomad4 OTH exome AF: 0.00535

GnomAD4 genome AF: 0.0278 AC: 4238 AN: 152246 Hom.: 226 Cov.: 32 AF XY: 0.0270 AC XY: 2013 AN XY: 74446

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.0108

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000162

Gnomad4 OTH AF: 0.0166

Alfa AF: 0.00255 Hom.: 28

Bravo AF: 0.0307

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.80

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

LitVar

Other links and lift over

dbSNP: rs6701920; hg19: chr1-160914917;