rs948100

Positions:

• chr11-117789560-C-G
• chr11-117789560-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.46+7474G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,182 control chromosomes in the GnomAD database, including 1,158 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 0.12 (1158 hom., cov: 32)
• Consequence: DSCAML1 NM_020693.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSCAML1	NM_020693.4	c.46+7474G>C		intron_variant		ENST00000651296.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSCAML1	ENST00000651296.2	c.46+7474G>C		intron_variant			NM_020693.4

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18043 AN: 152066 Hom.: 1152 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.119 AC: 18067 AN: 152182 Hom.: 1158 Cov.: 32 AF XY: 0.119 AC XY: 8879 AN XY: 74414

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0932

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0285 Hom.: 30

Bravo AF: 0.122

Asia WGS AF: 0.137 AC: 476 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	1.1
DANN	Benign	0.49

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: rs948100; hg19: chr11-117660275;