rs362698

Positions:

• chr7-103636845-T-C

Variant summary

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

The NM_005045.4(RELN):​c.2070-377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,238 control chromosomes in the GnomAD database, including 1,881 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 0.15 (1881 hom., cov: 32)
• Consequence: RELN NM_005045.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

Genes affected

RELN (HGNC:9957): (reelin) This gene encodes a large secreted extracellular matrix protein thought to control cell-cell interactions critical for cell positioning and neuronal migration during brain development. This protein may be involved in schizophrenia, autism, bipolar disorder, major depression and in migration defects associated with temporal lobe epilepsy. Mutations of this gene are associated with autosomal recessive lissencephaly with cerebellar hypoplasia. Two transcript variants encoding distinct isoforms have been identified for this gene. Other transcript variants have been described but their full length nature has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RELN	NM_005045.4	c.2070-377A>G		intron_variant		ENST00000428762.6
RELN	NM_173054.3	c.2070-377A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RELN	ENST00000428762.6	c.2070-377A>G		intron_variant		5	NM_005045.4	P5

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22715 AN: 152120 Hom.: 1879 Cov.: 32

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.149 AC: 22722 AN: 152238 Hom.: 1881 Cov.: 32 AF XY: 0.153 AC XY: 11410 AN XY: 74434

Gnomad4 AFR AF: 0.0931

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.155

Alfa AF: 0.157 Hom.: 3000

Bravo AF: 0.147

Asia WGS AF: 0.250 AC: 867 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.47
DANN	Benign	0.52

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: rs362698; hg19: chr7-103277292;