chr2-124155940-G-A

Variant names:

• chr2-124155940-G-A
• rs960537
• NM_001367498.1:c.83-65765G>A

Variant summary

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

The NM_001367498.1(CNTNAP5):​c.83-65765G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0689 in 152,326 control chromosomes in the GnomAD database, including 558 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 0.069 (558 hom., cov: 33)
• Consequence: CNTNAP5 NM_001367498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367498.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTNAP5	NM_001367498.1	MANE Select	c.83-65765G>A		intron	N/A	NP_001354427.1
	CNTNAP5	NM_130773.4		c.83-65765G>A		intron	N/A	NP_570129.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTNAP5	ENST00000682447.1	MANE Select	c.83-65765G>A		intron	N/A	ENSP00000508115.1
	CNTNAP5	ENST00000431078.1	TSL:1	c.83-65765G>A		intron	N/A	ENSP00000399013.1

Frequencies

GnomAD3 genomes AF: 0.0689 AC: 10480 AN: 152208 Hom.: 555 Cov.: 33

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0829

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0689 AC: 10490 AN: 152326 Hom.: 558 Cov.: 33 AF XY: 0.0705 AC XY: 5248 AN XY: 74470

African (AFR) AF: 0.0167 AC: 694 AN: 41592

American (AMR) AF: 0.0463 AC: 708 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 487 AN: 3472

East Asian (EAS) AF: 0.240 AC: 1239 AN: 5162

South Asian (SAS) AF: 0.177 AC: 853 AN: 4828

European-Finnish (FIN) AF: 0.0628 AC: 667 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5639 AN: 68032

Other (OTH) AF: 0.0743 AC: 157 AN: 2114

Alfa AF: 0.0789 Hom.: 1093

Bravo AF: 0.0635

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.49
PhyloP100		-0.85
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: rs960537; hg19: chr2-124913517;