NM_144622.3:c.2106-153A>G

Variant names:

• chr1-155018913-T-C
• rs905938
• NM_144622.3:c.2106-153A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144622.3(DCST2):​c.2106-153A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,024 control chromosomes in the GnomAD database, including 4,534 homozygotes. 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: 𝑓 0.24 (4534 hom., cov: 32)
• Consequence: DCST2 NM_144622.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 56 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144622.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCST2	NM_144622.3	MANE Select	c.2106-153A>G		intron	N/A	NP_653223.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCST2	ENST00000368424.4	TSL:1 MANE Select	c.2106-153A>G		intron	N/A	ENSP00000357409.3
	DCST2	ENST00000368423.5	TSL:2	n.1858-153A>G		intron	N/A
	DCST2	ENST00000467991.2	TSL:4	n.*350-153A>G		intron	N/A	ENSP00000437330.2

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36310 AN: 151906 Hom.: 4528 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0577

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.239 AC: 36343 AN: 152024 Hom.: 4534 Cov.: 32 AF XY: 0.233 AC XY: 17339 AN XY: 74316

African (AFR) AF: 0.272 AC: 11259 AN: 41454

American (AMR) AF: 0.163 AC: 2497 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3468

East Asian (EAS) AF: 0.0578 AC: 299 AN: 5170

South Asian (SAS) AF: 0.146 AC: 702 AN: 4816

European-Finnish (FIN) AF: 0.229 AC: 2421 AN: 10576

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17569 AN: 67928

Other (OTH) AF: 0.237 AC: 499 AN: 2108

Alfa AF: 0.249 Hom.: 11853

Bravo AF: 0.236

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.76
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs905938; hg19: chr1-154991389;