chr10-97117184-G-A

Variant names:

• chr10-97117184-G-A
• rs2636788
• NM_003061.3:c.413+40634C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003061.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLIT1	NM_003061.3	MANE Select	c.413+40634C>T		intron	N/A	NP_003052.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLIT1	ENST00000266058.9	TSL:1 MANE Select	c.413+40634C>T		intron	N/A	ENSP00000266058.4
	SLIT1	ENST00000371070.8	TSL:5	c.413+40634C>T		intron	N/A	ENSP00000360109.4
	SLIT1	ENST00000314867.9	TSL:5	c.362+40634C>T		intron	N/A	ENSP00000315005.5

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

African (AFR) AF: 0.714 AC: 29579 AN: 41456

American (AMR) AF: 0.852 AC: 13028 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2906 AN: 3470

East Asian (EAS) AF: 0.734 AC: 3792 AN: 5166

South Asian (SAS) AF: 0.840 AC: 4035 AN: 4806

European-Finnish (FIN) AF: 0.847 AC: 8967 AN: 10582

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57203 AN: 68008

Other (OTH) AF: 0.809 AC: 1709 AN: 2112

Alfa AF: 0.825 Hom.: 209250

Bravo AF: 0.799

Asia WGS AF: 0.749 AC: 2605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.88
DANN	Benign	0.60
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2636788; hg19: chr10-98876941;