chr11-117724796-C-T

Position:

• chr11-117724796-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+51995G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,234 control chromosomes in the GnomAD database, including 2,145 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 0.15 (2145 hom., cov: 33)
• Consequence: DSCAML1 NM_020693.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DSCAML1	NM_020693.4	c.511+51995G>A		intron_variant		ENST00000651296.2	NP_065744.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSCAML1	ENST00000651296.2	c.511+51995G>A		intron_variant			NM_020693.4	ENSP00000498769.1
DSCAML1	ENST00000321322.6	c.691+51995G>A		intron_variant		1		ENSP00000315465.6
DSCAML1	ENST00000651172.1	c.691+51995G>A		intron_variant				ENSP00000498407.1
DSCAML1	ENST00000527706.5	c.102+55959G>A		intron_variant		5		ENSP00000434335.1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22572 AN: 152116 Hom.: 2148 Cov.: 33

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.148 AC: 22559 AN: 152234 Hom.: 2145 Cov.: 33 AF XY: 0.154 AC XY: 11464 AN XY: 74408

Gnomad4 AFR AF: 0.0365

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.155

Alfa AF: 0.168 Hom.: 4724

Bravo AF: 0.141

Asia WGS AF: 0.216 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.071
DANN	Benign	0.18

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: rs11216517; hg19: chr11-117595511;