16-68644843-A-G

Position:

• chr16-68644843-A-G

Variant summary

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

The ENST00000562172.2(CDH3-AS1):​n.1087T>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 0.218 in 157,598 control chromosomes in the GnomAD database, including 4,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.22 (4060 hom., cov: 32)
  • Exomes 𝑓: 0.14 (85 hom.)
• Consequence: CDH3-AS1 ENST00000562172.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.502

Genes affected

CDH3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 16-68644843-A-G is Benign according to our data. Variant chr16-68644843-A-G is described in ClinVar as [Benign]. Clinvar id is 320212.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH3-AS1	NR_186394.1	n.1120T>C		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.1087T>C		non_coding_transcript_exon_variant	2/2	3
CDH3	ENST00000565453.1	n.223-166A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33516 AN: 151810 Hom.: 4054 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.139 AC: 792 AN: 5688 Hom.: 85 Cov.: 0 AF XY: 0.143 AC XY: 421 AN XY: 2950

Gnomad4 AFR exome AF: 0.192

Gnomad4 AMR exome AF: 0.120

Gnomad4 ASJ exome AF: 0.148

Gnomad4 EAS exome AF: 0.0500

Gnomad4 SAS exome AF: 0.0814

Gnomad4 FIN exome AF: 0.0804

Gnomad4 NFE exome AF: 0.161

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.221 AC: 33552 AN: 151910 Hom.: 4060 Cov.: 32 AF XY: 0.217 AC XY: 16077 AN XY: 74208

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.218

Alfa AF: 0.209 Hom.: 5422

Bravo AF: 0.221

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

EEM syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.68

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: rs11644435; hg19: chr16-68678746;