chr1-155018913-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCST2	NM_144622.3	c.2106-153A>G		intron_variant	Intron 14 of 14	ENST00000368424.4	NP_653223.2
DCST2	XM_011509188.3	c.1446-153A>G		intron_variant	Intron 12 of 12		XP_011507490.1
DCST2	XM_047445576.1	c.1446-153A>G		intron_variant	Intron 12 of 12		XP_047301532.1
DCST2	XM_011509189.3	c.1110-153A>G		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>G		intron_variant	Intron 14 of 14	1	NM_144622.3	ENSP00000357409.3
DCST2	ENST00000368423.5	n.1858-153A>G		intron_variant	Intron 9 of 9	2
DCST2	ENST00000467991.2	n.*350-153A>G		intron_variant	Intron 4 of 4	4		ENSP00000437330.2
DCST2	ENST00000485982.5	n.*254-153A>G		intron_variant	Intron 15 of 15	2		ENSP00000436964.1

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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0578

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.237

Alfa AF: 0.250 Hom.: 3421

Bravo AF: 0.236

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs905938; hg19: chr1-154991389;