NM_003061.3:c.414-45762C>T

Variant names:

• chr10-97111848-G-A
• rs2817698
• NM_003061.3:c.414-45762C>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.414-45762C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,838 control chromosomes in the GnomAD database, including 30,468 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 0.62 (30468 hom., cov: 31)
• Consequence: SLIT1 NM_003061.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 3 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=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLIT1	NM_003061.3	c.414-45762C>T		intron_variant	Intron 4 of 36	ENST00000266058.9	NP_003052.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLIT1	ENST00000266058.9	c.414-45762C>T		intron_variant	Intron 4 of 36	1	NM_003061.3	ENSP00000266058.4
SLIT1	ENST00000371070.8	c.414-45762C>T		intron_variant	Intron 4 of 36	5		ENSP00000360109.4
SLIT1	ENST00000314867.9	c.363-45762C>T		intron_variant	Intron 4 of 21	5		ENSP00000315005.5
SLIT1	ENST00000371041.3	c.414-45762C>T		intron_variant	Intron 4 of 11	2		ENSP00000360080.3

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94756 AN: 151716 Hom.: 30448 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.624 AC: 94814 AN: 151838 Hom.: 30468 Cov.: 31 AF XY: 0.628 AC XY: 46580 AN XY: 74226

African (AFR) AF: 0.469 AC: 19383 AN: 41362

American (AMR) AF: 0.703 AC: 10716 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3485 AN: 5138

South Asian (SAS) AF: 0.697 AC: 3337 AN: 4788

European-Finnish (FIN) AF: 0.695 AC: 7334 AN: 10558

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46288 AN: 67960

Other (OTH) AF: 0.630 AC: 1329 AN: 2108

Alfa AF: 0.663 Hom.: 143520

Bravo AF: 0.621

Asia WGS AF: 0.627 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	6.5
DANN	Benign	0.84
PhyloP100		-0.56
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: rs2817698; hg19: chr10-98871605;