chr16-83807608-G-T

Position:

• chr16-83807608-G-T

Variant summary

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

The ENST00000561599.2(CDH13-AS2):​n.227C>A 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 0.24 in 160,976 control chromosomes in the GnomAD database, including 5,053 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.24 (4822 hom., cov: 32)
  • Exomes 𝑓: 0.20 (231 hom.)
• Consequence: CDH13-AS2 ENST00000561599.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.60

Genes affected

CDH13-AS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 16-83807608-G-T is Benign according to our data. Variant chr16-83807608-G-T is described in ClinVar as [Benign]. Clinvar id is 1226958.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.83807608G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH13-AS2	ENST00000561599.2	n.227C>A		non_coding_transcript_exon_variant	1/5	4
HSBP1	ENST00000690173.1	n.98-427G>T		intron_variant
HSBP1	ENST00000693379.1	n.98-427G>T		intron_variant
HSBP1	ENST00000693758.1	n.98-427G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36815 AN: 151900 Hom.: 4822 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.200 AC: 1788 AN: 8958 Hom.: 231 Cov.: 0 AF XY: 0.198 AC XY: 978 AN XY: 4948

Gnomad4 AFR exome AF: 0.185

Gnomad4 AMR exome AF: 0.168

Gnomad4 ASJ exome AF: 0.144

Gnomad4 EAS exome AF: 0.0758

Gnomad4 SAS exome AF: 0.188

Gnomad4 FIN exome AF: 0.178

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.189

GnomAD4 genome AF: 0.242 AC: 36825 AN: 152018 Hom.: 4822 Cov.: 32 AF XY: 0.243 AC XY: 18033 AN XY: 74296

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0979

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.235

Alfa AF: 0.240 Hom.: 1457

Bravo AF: 0.232

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -
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	-0.82
CADD	Benign	4.4
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: rs11149602; hg19: chr16-83841213;