rs10892151

chr11-117661016-C-T

Variant summary

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

The NM_020693.4(DSCAML1):c.511+115775G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 152,230 control chromosomes in the GnomAD database, including 1,420 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 0.093 (1420 hom., cov: 32)
• Consequence: DSCAML1 NM_020693.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSCAML1	NM_020693.4	c.511+115775G>A		intron_variant		ENST00000651296.2
LOC105369515	XR_948060.3	n.71+1890C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSCAML1	ENST00000651296.2	c.511+115775G>A		intron_variant			NM_020693.4
DSCAML1	ENST00000321322.6	c.691+115775G>A		intron_variant		1		P1
DSCAML1	ENST00000527706.5	c.102+119739G>A		intron_variant		5
DSCAML1	ENST00000651172.1	c.691+115775G>A		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14160 AN: 152112 Hom.: 1414 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0500

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0165

Gnomad SAS AF: 0.0398

Gnomad FIN AF: 0.0326

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0932 AC: 14187 AN: 152230 Hom.: 1420 Cov.: 32 AF XY: 0.0915 AC XY: 6811 AN XY: 74432

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.0499

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.0326

Gnomad4 NFE AF: 0.0286

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0387 Hom.: 412

Bravo AF: 0.101

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.8
Dann	Benign	0.48

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: rs10892151; hg19: chr11-117531731;