NM_020693.4:c.2141A>G

Variant names:

• chr11-117504965-T-C
• rs193920955
• NM_020693.4:c.2141A>G

Variant summary

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

The NM_020693.4(DSCAML1):​c.2141A>G​(p.Asp714Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: DSCAML1 NM_020693.4 missense
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 8.01

Genes affected

DSCAML1 (HGNC:14656): (DS cell adhesion molecule like 1) The protein encoded by this gene is a member of the Ig superfamily of cell adhesion molecules and is involved in neuronal differentiation. The encoded membrane-bound protein localizes to the cell surface, where it forms aggregates that repel neuronal processes of the same cell type. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSCAML1	NM_020693.4	c.2141A>G	p.Asp714Gly	missense_variant	Exon 10 of 33	ENST00000651296.2	NP_065744.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSCAML1	ENST00000651296.2	c.2141A>G	p.Asp714Gly	missense_variant	Exon 10 of 33		NM_020693.4	ENSP00000498769.1
DSCAML1	ENST00000321322.6	c.2321A>G	p.Asp774Gly	missense_variant	Exon 10 of 33	1		ENSP00000315465.6
DSCAML1	ENST00000651172.1	c.2321A>G	p.Asp774Gly	missense_variant	Exon 10 of 33			ENSP00000498407.1
DSCAML1	ENST00000527706.5	c.1511A>G	p.Asp504Gly	missense_variant	Exon 8 of 31	5		ENSP00000434335.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Malignant tumor of prostate Uncertain:1

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Science for Life laboratory, Karolinska Institutet

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.63
BayesDel_addAF	Benign	-0.039	T
BayesDel_noAF	Benign	-0.29
CADD	Uncertain	25
DANN	Uncertain	1.0
Eigen	Benign	0.043
Eigen_PC	Benign	0.095
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.92	D;D
M_CAP	Benign	0.044	D
MetaRNN	Uncertain	0.51	D;D
MetaSVM	Benign	-0.85	T
PrimateAI	Pathogenic	0.85	D
PROVEAN	Uncertain	-4.2	D;D
REVEL	Benign	0.27
Sift	Benign	0.15	T;D
Sift4G	Uncertain	0.012	D;D
Vest4		0.56
MVP		0.62
MPC		1.0
ClinPred		0.96	D
GERP RS		3.2
gMVP		0.54

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

LitVar

Other links and lift over

dbSNP: rs193920955; hg19: chr11-117375680; COSMIC: COSV58386097;