2-124362616-T-G

Variant names:

• chr2-124362616-T-G
• rs11688892
• NM_001367498.1:c.382-54827T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367498.1(CNTNAP5):​c.382-54827T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0705 in 152,256 control chromosomes in the GnomAD database, including 481 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 0.070 (481 hom., cov: 33)
• Consequence: CNTNAP5 NM_001367498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTNAP5	NM_001367498.1	c.382-54827T>G		intron_variant	Intron 3 of 23	ENST00000682447.1	NP_001354427.1
CNTNAP5	NM_130773.4	c.382-54827T>G		intron_variant	Intron 3 of 23		NP_570129.1
CNTNAP5	XM_017003316.2	c.382-54827T>G		intron_variant	Intron 3 of 22		XP_016858805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTNAP5	ENST00000682447.1	c.382-54827T>G		intron_variant	Intron 3 of 23		NM_001367498.1	ENSP00000508115.1
CNTNAP5	ENST00000431078.1	c.382-54827T>G		intron_variant	Intron 3 of 23	1		ENSP00000399013.1

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 10718 AN: 152138 Hom.: 483 Cov.: 33

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0450

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0557

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0705 AC: 10733 AN: 152256 Hom.: 481 Cov.: 33 AF XY: 0.0710 AC XY: 5284 AN XY: 74452

African (AFR) AF: 0.0822 AC: 3415 AN: 41550

American (AMR) AF: 0.0511 AC: 782 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1129 AN: 5164

South Asian (SAS) AF: 0.113 AC: 546 AN: 4832

European-Finnish (FIN) AF: 0.0450 AC: 477 AN: 10610

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0557 AC: 3786 AN: 68016

Other (OTH) AF: 0.0744 AC: 157 AN: 2110

Alfa AF: 0.0475 Hom.: 104

Bravo AF: 0.0720

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.41
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11688892; hg19: chr2-125120193;