rs2636788

chr10-97117184-G-A

Variant summary

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

The NM_003061.3(SLIT1):c.413+40634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,104 control chromosomes in the GnomAD database, including 49,355 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 0.80 (49355 hom., cov: 31)
• Consequence: SLIT1 NM_003061.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

Genes affected

SLIT1 (HGNC:11085): (slit guidance ligand 1) Enables Roundabout binding activity. Involved in axon extension involved in axon guidance; motor neuron axon guidance; and negative chemotaxis. Predicted to be located in extracellular region. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

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 (AMR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLIT1	NM_003061.3	c.413+40634C>T		intron_variant		ENST00000266058.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLIT1	ENST00000266058.9	c.413+40634C>T		intron_variant		1	NM_003061.3	P1
SLIT1	ENST00000314867.9	c.362+40634C>T		intron_variant		5
SLIT1	ENST00000371041.3	c.413+40634C>T		intron_variant		2
SLIT1	ENST00000371070.8	c.413+40634C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122139 AN: 151986 Hom.: 49310 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.804 AC: 122244 AN: 152104 Hom.: 49355 Cov.: 31 AF XY: 0.805 AC XY: 59812 AN XY: 74346

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.809

Alfa AF: 0.829 Hom.: 104362

Bravo AF: 0.799

Asia WGS AF: 0.749 AC: 2605 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	0.88
Dann	Benign	0.60

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: rs2636788; hg19: chr10-98876941;