chr16-68644734-C-CA

Position:

• chr16-68644734-C-CA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000562172.2(CDH3-AS1):​n.1195_1196insT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0013 (0 hom., cov: 18)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CDH3-AS1 ENST00000562172.2 non_coding_transcript_exon
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.786

Genes affected

CDH3-AS1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH3-AS1	NR_186394.1	n.1228_1229insT		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH3-AS1	ENST00000562172.2	n.1195_1196insT		non_coding_transcript_exon_variant	2/2	3
CDH3	ENST00000565453.1	n.223-275_223-274insA		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 94 AN: 74510 Hom.: 0 Cov.: 18 FAILED QC

Gnomad AFR AF: 0.000276

Gnomad AMI AF: 0.00365

Gnomad AMR AF: 0.00168

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000846

Gnomad SAS AF: 0.00191

Gnomad FIN AF: 0.00438

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00172

Gnomad OTH AF: 0.00105

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1076 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 564

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00126 AC: 94 AN: 74556 Hom.: 0 Cov.: 18 AF XY: 0.00130 AC XY: 46 AN XY: 35406

Gnomad4 AFR AF: 0.000276

Gnomad4 AMR AF: 0.00168

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000850

Gnomad4 SAS AF: 0.00191

Gnomad4 FIN AF: 0.00438

Gnomad4 NFE AF: 0.00172

Gnomad4 OTH AF: 0.00104

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

EEM syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs886052221; hg19: chr16-68678637;