rs39401

chr7-103854946-A-G

Variant summary

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

The NM_005045.4(RELN):c.338-21274T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,204 control chromosomes in the GnomAD database, including 5,504 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 0.26 (5504 hom., cov: 33)
• Consequence: RELN NM_005045.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RELN	NM_005045.4	c.338-21274T>C		intron_variant		ENST00000428762.6
RELN	NM_173054.3	c.338-21274T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RELN	ENST00000428762.6	c.338-21274T>C		intron_variant		5	NM_005045.4	P5

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39712 AN: 152086 Hom.: 5503 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0369

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.261 AC: 39731 AN: 152204 Hom.: 5504 Cov.: 33 AF XY: 0.256 AC XY: 19079 AN XY: 74398

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.0370

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.235

Alfa AF: 0.286 Hom.: 8659

Bravo AF: 0.255

Asia WGS AF: 0.138 AC: 479 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.7
Dann	Benign	0.72

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: rs39401; hg19: chr7-103495393;