chr2-124699663-A-G

Variant names:

• chr2-124699663-A-G
• rs7580383
• NM_001367498.1:c.2078-47566A>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.2078-47566A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,708 control chromosomes in the GnomAD database, including 13,686 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 0.41 (13686 hom., cov: 32)
• Consequence: CNTNAP5 NM_001367498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTNAP5	NM_001367498.1	c.2078-47566A>G		intron_variant	Intron 13 of 23	ENST00000682447.1	NP_001354427.1
CNTNAP5	NM_130773.4	c.2075-47566A>G		intron_variant	Intron 13 of 23		NP_570129.1
CNTNAP5	XM_017003316.2	c.2078-47566A>G		intron_variant	Intron 13 of 22		XP_016858805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTNAP5	ENST00000682447.1	c.2078-47566A>G		intron_variant	Intron 13 of 23		NM_001367498.1	ENSP00000508115.1
CNTNAP5	ENST00000431078.1	c.2075-47566A>G		intron_variant	Intron 13 of 23	1		ENSP00000399013.1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62589 AN: 151590 Hom.: 13653 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.00791

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.413 AC: 62669 AN: 151708 Hom.: 13686 Cov.: 32 AF XY: 0.402 AC XY: 29778 AN XY: 74142

African (AFR) AF: 0.490 AC: 20255 AN: 41306

American (AMR) AF: 0.333 AC: 5070 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1356 AN: 3462

East Asian (EAS) AF: 0.00792 AC: 41 AN: 5174

South Asian (SAS) AF: 0.290 AC: 1394 AN: 4810

European-Finnish (FIN) AF: 0.362 AC: 3822 AN: 10544

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29359 AN: 67856

Other (OTH) AF: 0.385 AC: 813 AN: 2110

Alfa AF: 0.426 Hom.: 45558

Bravo AF: 0.416

Asia WGS AF: 0.155 AC: 541 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		-0.23
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: rs7580383; hg19: chr2-125457240;