rs1874

Positions:

• chr11-126774308-G-A
• chr11-126774308-G-C
• chr11-126774308-G-T

Variant summary

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

The ENST00000525144.7(KIRREL3):​c.56-211396C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,856 control chromosomes in the GnomAD database, including 6,321 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 0.25 (6321 hom., cov: 30)
• Consequence: KIRREL3 ENST00000525144.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.619

Genes affected

KIRREL3 (HGNC:23204): (kirre like nephrin family adhesion molecule 3) The protein encoded by this gene is a member of the nephrin-like protein family. These proteins are expressed in fetal and adult brain, and also in podocytes of kidney glomeruli. The cytoplasmic domains of these proteins interact with the C-terminus of podocin, also expressed in the podocytes, cells involved in ensuring size- and charge-selective ultrafiltration. The protein encoded by this gene is a synaptic cell adhesion molecule with multiple extracellular immunoglobulin-like domains and a cytoplasmic PDZ domain-binding motif. Mutations in this gene are associated with several neurological and cognitive disorders. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

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 = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIRREL3	NM_032531.4	c.56-211396C>T		intron_variant		ENST00000525144.7	NP_115920.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIRREL3	ENST00000525144.7	c.56-211396C>T		intron_variant		1	NM_032531.4	ENSP00000435466	P4

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38128 AN: 151736 Hom.: 6317 Cov.: 30

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.251 AC: 38148 AN: 151856 Hom.: 6321 Cov.: 30 AF XY: 0.260 AC XY: 19269 AN XY: 74194

Gnomad4 AFR AF: 0.0811

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.281

Alfa AF: 0.265 Hom.: 7564

Bravo AF: 0.248

Asia WGS AF: 0.571 AC: 1980 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	5.7
DANN	Benign	0.66

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: rs1874; hg19: chr11-126644203;