10-100229753-C-T

Position:

• chr10-100229753-C-T

Variant summary

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

The ENST00000667469.1(CHUK-DT):​n.96+29C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0593 in 576,216 control chromosomes in the GnomAD database, including 1,358 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.075 (583 hom., cov: 32)
  • Exomes 𝑓: 0.054 (775 hom.)
• Consequence: CHUK-DT ENST00000667469.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.777

Genes affected

CHUK-DT (HGNC:55813): (CHUK divergent transcript)

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 10-100229753-C-T is Benign according to our data. Variant chr10-100229753-C-T is described in ClinVar as [Benign]. Clinvar id is 1181190.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHUK-DT	ENST00000667469.1	n.96+29C>T		intron_variant, non_coding_transcript_variant
CHUK-DT	ENST00000444359.1	n.58+29C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0750 AC: 11410 AN: 152136 Hom.: 584 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0555

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0472

Gnomad OTH AF: 0.0731

GnomAD4 exome AF: 0.0536 AC: 22741 AN: 423962 Hom.: 775 Cov.: 0 AF XY: 0.0533 AC XY: 11916 AN XY: 223538

Gnomad4 AFR exome AF: 0.144

Gnomad4 AMR exome AF: 0.0496

Gnomad4 ASJ exome AF: 0.0536

Gnomad4 EAS exome AF: 0.0686

Gnomad4 SAS exome AF: 0.0590

Gnomad4 FIN exome AF: 0.0535

Gnomad4 NFE exome AF: 0.0464

Gnomad4 OTH exome AF: 0.0623

GnomAD4 genome AF: 0.0750 AC: 11422 AN: 152254 Hom.: 583 Cov.: 32 AF XY: 0.0745 AC XY: 5549 AN XY: 74436

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.0559

Gnomad4 SAS AF: 0.0645

Gnomad4 FIN AF: 0.0555

Gnomad4 NFE AF: 0.0472

Gnomad4 OTH AF: 0.0733

Alfa AF: 0.0511 Hom.: 245

Bravo AF: 0.0771

Asia WGS AF: 0.0860 AC: 298 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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12770784; hg19: chr10-101989510;