chrX-154764902-T-C

Variant names:

• chrX-154764902-T-C
• rs782343800
• NM_001363.5:c.20T>C

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Moderate BP6 BS2

The NM_001363.5(DKC1):​c.20T>C​(p.Ile7Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000736 in 1,086,328 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. I7I) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0000074 (0 hom. 3 hem.)
• Consequence: DKC1 NM_001363.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1
• Conservation: PhyloP100: 1.25
• Publications: 0 publications found

Genes affected

DKC1 (HGNC:2890): (dyskerin pseudouridine synthase 1) This gene functions in two distinct complexes. It plays an active role in telomerase stabilization and maintenance, as well as recognition of snoRNAs containing H/ACA sequences which provides stability during biogenesis and assembly into H/ACA small nucleolar RNA ribonucleoproteins (snoRNPs). This gene is highly conserved and widely expressed, and may play additional roles in nucleo-cytoplasmic shuttling, DNA damage response, and cell adhesion. Mutations have been associated with X-linked dyskeratosis congenita. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

DKC1 Gene-Disease associations (from GenCC):

• DKC1-related disorder

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• dyskeratosis congenita, X-linked

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P
• dyskeratosis congenita

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Hoyeraal-Hreidarsson syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.13059404).
• BP6: Variant X-154764902-T-C is Benign according to our data. Variant chrX-154764902-T-C is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 459584.
• BS2: High AC in GnomAdExome4 at 8 XL,AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DKC1	NM_001363.5	MANE Select	c.20T>C	p.Ile7Thr	missense	Exon 2 of 15	NP_001354.1
	DKC1	NM_001142463.3		c.20T>C	p.Ile7Thr	missense	Exon 2 of 15	NP_001135935.1
	DKC1	NM_001288747.2		c.20T>C	p.Ile7Thr	missense	Exon 2 of 14	NP_001275676.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DKC1	ENST00000369550.10	TSL:1 MANE Select	c.20T>C	p.Ile7Thr	missense	Exon 2 of 15	ENSP00000358563.5
	DKC1	ENST00000620277.4	TSL:1	n.244T>C		non_coding_transcript_exon	Exon 2 of 14
	DKC1	ENST00000953351.1		c.20T>C	p.Ile7Thr	missense	Exon 2 of 15	ENSP00000623410.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD2 exomes AF: 0.0000491 AC: 9 AN: 183320 AF XY: 0.0000295

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000328

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000736 AC: 8 AN: 1086328 Hom.: 0 Cov.: 28 AF XY: 0.00000851 AC XY: 3 AN XY: 352548

African (AFR) AF: 0.00 AC: 0 AN: 26190

American (AMR) AF: 0.000227 AC: 8 AN: 35185

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19298

East Asian (EAS) AF: 0.00 AC: 0 AN: 30146

South Asian (SAS) AF: 0.00 AC: 0 AN: 53850

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40503

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4102

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 831342

Other (OTH) AF: 0.00 AC: 0 AN: 45712

GnomAD4 genome Cov.: 23

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.0000189

ExAC AF: 0.00000824 AC: 1

ClinVar

ClinVar submissions as Germline

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
-	-	1	Dyskeratosis congenita (1)
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.080	T
BayesDel_noAF	Uncertain	-0.040
CADD	Benign	8.6
DANN	Benign	0.74
DEOGEN2	Benign	0.18	T
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.56	T
M_CAP	Benign	0.040	D
MetaRNN	Benign	0.13	T
MetaSVM	Uncertain	-0.055	T
MutationAssessor	Benign	0.90	L
PhyloP100		1.2
PrimateAI	Uncertain	0.49	T
PROVEAN	Benign	0.36	N
REVEL	Uncertain	0.43
Sift	Uncertain	0.012	D
Sift4G	Benign	0.67	T
Polyphen		0.0	B
Vest4		0.27
MutPred		0.20		Loss of sheet (P = 0.0228)
MVP		0.98
MPC		1.6
ClinPred		0.023	T
GERP RS		0.30
PromoterAI		0.0094	Neutral
Varity_R		0.10
gMVP		0.32
Mutation Taster		=96/4	polymorphism

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

Other links and lift over

dbSNP: rs782343800; hg19: chrX-153993177;