rs373745947

Variant names:

• chr1-155048093-C-A
• NM_152494.4:c.1792C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-155048093-C-A
• chr1-155048093-C-G
• chr1-155048093-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_152494.4(DCST1):​c.1792C>A​(p.Leu598Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: DCST1 NM_152494.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375

Genes affected

DCST1 (HGNC:26539): (DC-STAMP domain containing 1) This gene encodes a protein with a domain similar to one found in dendritic cells (PMID:11169400) which play a key role in antigen processing and display for immune responses. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

DCST1-AS1 (HGNC:41147): (DCST1 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15472415).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCST1	NM_152494.4	c.1792C>A	p.Leu598Ile	missense_variant	Exon 16 of 17	ENST00000295542.6	NP_689707.2
DCST1	NM_001143687.2	c.1717C>A	p.Leu573Ile	missense_variant	Exon 15 of 16		NP_001137159.1
DCST1-AS1	NR_040772.1	n.652+1176G>T		intron_variant	Intron 2 of 3
DCST1-AS1	NR_040773.1	n.328+1176G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCST1	ENST00000295542.6	c.1792C>A	p.Leu598Ile	missense_variant	Exon 16 of 17	2	NM_152494.4	ENSP00000295542.2
DCST1	ENST00000525273.5	n.*144C>A		non_coding_transcript_exon_variant	Exon 15 of 15	2		ENSP00000433667.1
DCST1	ENST00000525273.5	n.*144C>A		3_prime_UTR_variant	Exon 15 of 15	2		ENSP00000433667.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461862 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727234

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	18
DANN	Benign	0.97
DEOGEN2	Benign	0.020	T;.;.
Eigen	Benign	-0.45
Eigen_PC	Benign	-0.53
FATHMM_MKL	Benign	0.090	N
LIST_S2	Benign	0.80	T;T;T
M_CAP	Benign	0.0058	T
MetaRNN	Benign	0.15	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.6	M;.;M
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	-0.73	N;N;N
REVEL	Benign	0.071
Sift	Benign	0.21	T;T;T
Sift4G	Benign	0.14	T;T;T
Polyphen		0.82	P;.;.
Vest4		0.46
MutPred		0.42		Gain of methylation at K601 (P = 0.0421);.;Gain of methylation at K601 (P = 0.0421);
MVP		0.18
MPC		0.41
ClinPred		0.47	T
GERP RS		3.9
Varity_R		0.13
gMVP		0.30

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-155020569;