11-1310024-G-C

Variant names:

• chr11-1310024-G-C
• rs5743854
• ENST00000530897.1:n.256G>C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NR_029409.1(TOLLIP-DT):​n.317G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,320 control chromosomes in the GnomAD database, including 51,411 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.82 (51388 hom., cov: 34)
  • Exomes 𝑓: 0.81 (23 hom.)
• Consequence: TOLLIP-DT NR_029409.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.994

Genes affected

TOLLIP-DT (HGNC:27403): (TOLLIP divergent transcript)

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 11-1310024-G-C is Benign according to our data. Variant chr11-1310024-G-C is described in ClinVar as [Benign]. Clinvar id is 1249282.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TOLLIP-DT	NR_029409.1	n.317G>C		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TOLLIP-DT	ENST00000530897.1	n.256G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124269 AN: 152132 Hom.: 51372 Cov.: 34

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.828

GnomAD4 exome AF: 0.814 AC: 57 AN: 70 Hom.: 23 Cov.: 0 AF XY: 0.810 AC XY: 47 AN XY: 58

Gnomad4 AFR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.833

Gnomad4 SAS exome AF: 0.833

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.818

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.817 AC: 124327 AN: 152250 Hom.: 51388 Cov.: 34 AF XY: 0.812 AC XY: 60444 AN XY: 74420

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.826

Alfa AF: 0.855 Hom.: 6965

Bravo AF: 0.815

Asia WGS AF: 0.688 AC: 2391 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jan 11, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 28463648) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5743854; hg19: chr11-1331254; COSMIC: COSV55136949;