10-100229692-G-T

Position:

• chr10-100229692-G-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.64G>T 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 0.0544 in 599,830 control chromosomes in the GnomAD database, including 1,987 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.088 (1166 hom., cov: 32)
  • Exomes 𝑓: 0.043 (821 hom.)
• Consequence: CHUK-DT ENST00000667469.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.148

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=-0.81).
• BP6: Variant 10-100229692-G-T is Benign according to our data. Variant chr10-100229692-G-T is described in ClinVar as [Benign]. Clinvar id is 1183088.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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.64G>T		non_coding_transcript_exon_variant	1/4
CHUK-DT	ENST00000444359.1	n.26G>T		non_coding_transcript_exon_variant	1/5	5

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13309 AN: 152150 Hom.: 1144 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.0956

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0208

Gnomad OTH AF: 0.0793

GnomAD4 exome AF: 0.0430 AC: 19244 AN: 447562 Hom.: 821 Cov.: 4 AF XY: 0.0433 AC XY: 10249 AN XY: 236958

Gnomad4 AFR exome AF: 0.222

Gnomad4 AMR exome AF: 0.0694

Gnomad4 ASJ exome AF: 0.0217

Gnomad4 EAS exome AF: 0.0963

Gnomad4 SAS exome AF: 0.0714

Gnomad4 FIN exome AF: 0.0680

Gnomad4 NFE exome AF: 0.0199

Gnomad4 OTH exome AF: 0.0498

GnomAD4 genome AF: 0.0878 AC: 13376 AN: 152268 Hom.: 1166 Cov.: 32 AF XY: 0.0913 AC XY: 6801 AN XY: 74474

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0666

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.0952

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.0208

Gnomad4 OTH AF: 0.0784

Alfa AF: 0.0252 Hom.: 36

Bravo AF: 0.0937

Asia WGS AF: 0.100 AC: 346 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	May 11, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.15
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: rs3829158; hg19: chr10-101989449;