chr2-124240787-G-T

Position:

• chr2-124240787-G-T

Variant summary

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

The NM_001367498.1(CNTNAP5):​c.188-1413G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 151,968 control chromosomes in the GnomAD database, including 3,028 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 0.19 (3028 hom., cov: 32)
• Consequence: CNTNAP5 NM_001367498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

CNTNAP5 (HGNC:18748): (contactin associated protein family member 5) This gene product belongs to the neurexin family, members of which function in the vertebrate nervous system as cell adhesion molecules and receptors. This protein, like other neurexin proteins, contains epidermal growth factor repeats and laminin G domains. In addition, it includes an F5/8 type C domain, discoidin/neuropilin- and fibrinogen-like domains, and thrombospondin N-terminal-like domains. [provided by RefSeq, Jul 2008]

CNTNAP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTNAP5	NM_001367498.1	c.188-1413G>T		intron_variant		ENST00000682447.1	NP_001354427.1
CNTNAP5	NM_130773.4	c.188-1413G>T		intron_variant			NP_570129.1
CNTNAP5	XM_017003316.2	c.188-1413G>T		intron_variant			XP_016858805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTNAP5	ENST00000682447.1	c.188-1413G>T		intron_variant			NM_001367498.1	ENSP00000508115.1
CNTNAP5	ENST00000431078.1	c.188-1413G>T		intron_variant		1		ENSP00000399013.1
CNTNAP5	ENST00000470921.1	n.106-1413G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29378 AN: 151848 Hom.: 3023 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.193 AC: 29397 AN: 151968 Hom.: 3028 Cov.: 32 AF XY: 0.190 AC XY: 14132 AN XY: 74260

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.216

Alfa AF: 0.226 Hom.: 4737

Bravo AF: 0.191

Asia WGS AF: 0.198 AC: 690 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.49

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: rs1367248; hg19: chr2-124998364;