rs13021885

Positions:

• chr2-124534260-C-T

Variant summary

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

The NM_001367498.1(CNTNAP5):​c.1649+6804C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.043 in 151,560 control chromosomes in the GnomAD database, including 190 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 0.043 (190 hom., cov: 32)
• Consequence: CNTNAP5 NM_001367498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTNAP5	NM_001367498.1	c.1649+6804C>T		intron_variant		ENST00000682447.1	NP_001354427.1
CNTNAP5	NM_130773.4	c.1646+6804C>T		intron_variant			NP_570129.1
CNTNAP5	XM_017003316.2	c.1649+6804C>T		intron_variant			XP_016858805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTNAP5	ENST00000682447.1	c.1649+6804C>T		intron_variant			NM_001367498.1	ENSP00000508115	A1
CNTNAP5	ENST00000431078.1	c.1646+6804C>T		intron_variant		1		ENSP00000399013	P4

Frequencies

GnomAD3 genomes AF: 0.0430 AC: 6518 AN: 151442 Hom.: 189 Cov.: 32

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.0401

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0571

Gnomad OTH AF: 0.0403

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

GnomAD4 genome AF: 0.0430 AC: 6519 AN: 151560 Hom.: 190 Cov.: 32 AF XY: 0.0428 AC XY: 3165 AN XY: 74002

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.0573

Gnomad4 ASJ AF: 0.0453

Gnomad4 EAS AF: 0.0404

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0259

Gnomad4 NFE AF: 0.0571

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0495 Hom.: 31

Bravo AF: 0.0435

Asia WGS AF: 0.0610 AC: 213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.48

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: rs13021885; hg19: chr2-125291837;