rs10892152

chr11-117661828-A-G

Variant summary

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

The NM_020693.4(DSCAML1):c.511+114963T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,128 control chromosomes in the GnomAD database, including 7,163 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 0.30 (7163 hom., cov: 32)
• Consequence: DSCAML1 NM_020693.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

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]

LOC105369515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSCAML1	NM_020693.4	c.511+114963T>C		intron_variant		ENST00000651296.2
LOC105369515	XR_948060.3	n.71+2702A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSCAML1	ENST00000651296.2	c.511+114963T>C		intron_variant			NM_020693.4
DSCAML1	ENST00000321322.6	c.691+114963T>C		intron_variant		1		P1
DSCAML1	ENST00000527706.5	c.102+118927T>C		intron_variant		5
DSCAML1	ENST00000651172.1	c.691+114963T>C		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45662 AN: 152010 Hom.: 7158 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0924

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.300 AC: 45686 AN: 152128 Hom.: 7163 Cov.: 32 AF XY: 0.303 AC XY: 22545 AN XY: 74356

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.0916

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.325

Alfa AF: 0.310 Hom.: 908

Bravo AF: 0.295

Asia WGS AF: 0.210 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.0040
Dann	Benign	0.41

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: rs10892152; hg19: chr11-117532543;