chr11-117570988-T-G

Position:

• chr11-117570988-T-G

Variant summary

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

The NM_020693.4(DSCAML1):​c.512-38466A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0154 in 152,364 control chromosomes in the GnomAD database, including 36 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 0.015 (36 hom., cov: 33)
• Consequence: DSCAML1 NM_020693.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSCAML1	NM_020693.4	c.512-38466A>C		intron_variant		ENST00000651296.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSCAML1	ENST00000651296.2	c.512-38466A>C		intron_variant			NM_020693.4
DSCAML1	ENST00000321322.6	c.692-38466A>C		intron_variant		1		P1
DSCAML1	ENST00000527706.5	c.103-45979A>C		intron_variant		5
DSCAML1	ENST00000651172.1	c.692-38466A>C		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.0154 AC: 2345 AN: 152246 Hom.: 36 Cov.: 33

Gnomad AFR AF: 0.00437

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0837

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0154 AC: 2347 AN: 152364 Hom.: 36 Cov.: 33 AF XY: 0.0151 AC XY: 1128 AN XY: 74512

Gnomad4 AFR AF: 0.00435

Gnomad4 AMR AF: 0.0170

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.0841

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.0150

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.00918 Hom.: 4

Bravo AF: 0.0168

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.8
DANN	Benign	0.77

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: rs10502226; hg19: chr11-117441703;