rs13021885

Variant names:

• chr2-124534260-C-T
• rs13021885
• NM_001367498.1:c.1649+6804C>T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.94).
• 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 rank	MANE	Protein	UniProt
CNTNAP5	NM_001367498.1	c.1649+6804C>T		intron_variant	Intron 10 of 23	ENST00000682447.1	NP_001354427.1
CNTNAP5	NM_130773.4	c.1646+6804C>T		intron_variant	Intron 10 of 23		NP_570129.1
CNTNAP5	XM_017003316.2	c.1649+6804C>T		intron_variant	Intron 10 of 22		XP_016858805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTNAP5	ENST00000682447.1	c.1649+6804C>T		intron_variant	Intron 10 of 23		NM_001367498.1	ENSP00000508115.1
CNTNAP5	ENST00000431078.1	c.1646+6804C>T		intron_variant	Intron 10 of 23	1		ENSP00000399013.1

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

African (AFR) AF: 0.0108 AC: 445 AN: 41310

American (AMR) AF: 0.0573 AC: 872 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0453 AC: 157 AN: 3466

East Asian (EAS) AF: 0.0404 AC: 207 AN: 5120

South Asian (SAS) AF: 0.103 AC: 493 AN: 4790

European-Finnish (FIN) AF: 0.0259 AC: 270 AN: 10426

Middle Eastern (MID) AF: 0.0552 AC: 16 AN: 290

European-Non Finnish (NFE) AF: 0.0571 AC: 3877 AN: 67916

Other (OTH) AF: 0.0398 AC: 84 AN: 2108

Alfa AF: 0.0435 Hom.: 91

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
PhyloP100		-0.72
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: rs13021885; hg19: chr2-125291837;