rs262375

chr7-103812610-G-A

Variant summary

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

The NM_005045.4(RELN):c.473+20927C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,056 control chromosomes in the GnomAD database, including 42,104 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 0.74 (42104 hom., cov: 31)
• Consequence: RELN NM_005045.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

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 (NFE) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RELN	NM_005045.4	c.473+20927C>T		intron_variant		ENST00000428762.6
RELN	NM_173054.3	c.473+20927C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RELN	ENST00000428762.6	c.473+20927C>T		intron_variant		5	NM_005045.4	P5

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112433 AN: 151938 Hom.: 42076 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.740 AC: 112511 AN: 152056 Hom.: 42104 Cov.: 31 AF XY: 0.742 AC XY: 55161 AN XY: 74316

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.738

Alfa AF: 0.777 Hom.: 61442

Bravo AF: 0.724

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.3
Dann	Benign	0.19

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: rs262375; hg19: chr7-103453057;