1-155018913-T-A

Variant names:

• chr1-155018913-T-A
• NM_144622.3:c.2106-153A>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_144622.3(DCST2):​c.2106-153A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts 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)
• Consequence: DCST2 NM_144622.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

DCST2 (HGNC:26562): (DC-STAMP domain containing 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCST2	NM_144622.3	c.2106-153A>T		intron_variant	Intron 14 of 14	ENST00000368424.4	NP_653223.2
DCST2	XM_011509188.3	c.1446-153A>T		intron_variant	Intron 12 of 12		XP_011507490.1
DCST2	XM_047445576.1	c.1446-153A>T		intron_variant	Intron 12 of 12		XP_047301532.1
DCST2	XM_011509189.3	c.1110-153A>T		intron_variant	Intron 9 of 9		XP_011507491.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCST2	ENST00000368424.4	c.2106-153A>T		intron_variant	Intron 14 of 14	1	NM_144622.3	ENSP00000357409.3
DCST2	ENST00000368423.5	n.1858-153A>T		intron_variant	Intron 9 of 9	2
DCST2	ENST00000467991.2	n.*350-153A>T		intron_variant	Intron 4 of 4	4		ENSP00000437330.2
DCST2	ENST00000485982.5	n.*254-153A>T		intron_variant	Intron 15 of 15	2		ENSP00000436964.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.62
DANN	Benign	0.82

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: chr1-154991389;