rs1367248

Variant names:

• chr2-124240787-G-T
• rs1367248
• NM_001367498.1:c.188-1413G>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.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
• Publications: 4 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=-0.91).
• 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 rank	MANE	Protein	UniProt
CNTNAP5	NM_001367498.1	c.188-1413G>T		intron_variant	Intron 2 of 23	ENST00000682447.1	NP_001354427.1
CNTNAP5	NM_130773.4	c.188-1413G>T		intron_variant	Intron 2 of 23		NP_570129.1
CNTNAP5	XM_017003316.2	c.188-1413G>T		intron_variant	Intron 2 of 22		XP_016858805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTNAP5	ENST00000682447.1	c.188-1413G>T		intron_variant	Intron 2 of 23		NM_001367498.1	ENSP00000508115.1
CNTNAP5	ENST00000431078.1	c.188-1413G>T		intron_variant	Intron 2 of 23	1		ENSP00000399013.1
CNTNAP5	ENST00000470921.1	n.106-1413G>T		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.129 AC: 5352 AN: 41480

American (AMR) AF: 0.178 AC: 2726 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1274 AN: 5134

South Asian (SAS) AF: 0.157 AC: 757 AN: 4820

European-Finnish (FIN) AF: 0.195 AC: 2055 AN: 10532

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15780 AN: 67944

Other (OTH) AF: 0.216 AC: 455 AN: 2108

Alfa AF: 0.218 Hom.: 11346

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
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: rs1367248; hg19: chr2-124998364;