rs498889

Positions:

• chr11-117588947-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020693.4(DSCAML1):​c.512-56425A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,068 control chromosomes in the GnomAD database, including 3,817 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 0.21 (3817 hom., cov: 32)
• Consequence: DSCAML1 NM_020693.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DSCAML1	NM_020693.4	c.512-56425A>G		intron_variant		ENST00000651296.2	NP_065744.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSCAML1	ENST00000651296.2	c.512-56425A>G		intron_variant			NM_020693.4	ENSP00000498769
DSCAML1	ENST00000321322.6	c.692-56425A>G		intron_variant		1		ENSP00000315465	P1
DSCAML1	ENST00000527706.5	c.103-63938A>G		intron_variant		5		ENSP00000434335
DSCAML1	ENST00000651172.1	c.692-56425A>G		intron_variant				ENSP00000498407	P1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32406 AN: 151950 Hom.: 3819 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.213 AC: 32418 AN: 152068 Hom.: 3817 Cov.: 32 AF XY: 0.218 AC XY: 16205 AN XY: 74342

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.229

Alfa AF: 0.223 Hom.: 523

Bravo AF: 0.209

Asia WGS AF: 0.301 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	17
DANN	Benign	0.64

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: rs498889; hg19: chr11-117459662;