chr10-97148976-C-A

Variant names:

• chr10-97148976-C-A
• rs7072055
• NM_003061.3:c.413+8842G>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+8842G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,200 control chromosomes in the GnomAD database, including 1,546 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 0.14 (1546 hom., cov: 33)
• Consequence: SLIT1 NM_003061.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• 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=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.182 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLIT1	NM_003061.3	MANE Select	c.413+8842G>T		intron	N/A	NP_003052.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLIT1	ENST00000266058.9	TSL:1 MANE Select	c.413+8842G>T		intron	N/A	ENSP00000266058.4
	SLIT1	ENST00000371070.8	TSL:5	c.413+8842G>T		intron	N/A	ENSP00000360109.4
	SLIT1	ENST00000314867.9	TSL:5	c.362+8842G>T		intron	N/A	ENSP00000315005.5

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21084 AN: 152082 Hom.: 1547 Cov.: 33

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.139 AC: 21086 AN: 152200 Hom.: 1546 Cov.: 33 AF XY: 0.140 AC XY: 10434 AN XY: 74398

African (AFR) AF: 0.0907 AC: 3767 AN: 41534

American (AMR) AF: 0.115 AC: 1763 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3472

East Asian (EAS) AF: 0.168 AC: 871 AN: 5180

South Asian (SAS) AF: 0.192 AC: 925 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1621 AN: 10574

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11051 AN: 68004

Other (OTH) AF: 0.146 AC: 308 AN: 2112

Alfa AF: 0.154 Hom.: 5098

Bravo AF: 0.135

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.2
DANN	Benign	0.88
PhyloP100		-0.60
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: rs7072055; hg19: chr10-98908733;