rs4848944

Variant names:

• chr2-124589780-A-C
• rs4848944
• NM_001367498.1:c.1757-20021A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-124589780-A-C
• chr2-124589780-A-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.1757-20021A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,984 control chromosomes in the GnomAD database, including 12,943 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 0.40 (12943 hom., cov: 32)
• Consequence: CNTNAP5 NM_001367498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.59 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.1757-20021A>C		intron	N/A	NP_001354427.1
	CNTNAP5	NM_130773.4		c.1754-20021A>C		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.1757-20021A>C		intron	N/A	ENSP00000508115.1
	CNTNAP5	ENST00000431078.1	TSL:1	c.1754-20021A>C		intron	N/A	ENSP00000399013.1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60877 AN: 151866 Hom.: 12928 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.401 AC: 60943 AN: 151984 Hom.: 12943 Cov.: 32 AF XY: 0.400 AC XY: 29731 AN XY: 74272

African (AFR) AF: 0.278 AC: 11513 AN: 41452

American (AMR) AF: 0.347 AC: 5303 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3466

East Asian (EAS) AF: 0.259 AC: 1332 AN: 5144

South Asian (SAS) AF: 0.609 AC: 2931 AN: 4816

European-Finnish (FIN) AF: 0.431 AC: 4544 AN: 10550

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32672 AN: 67976

Other (OTH) AF: 0.372 AC: 785 AN: 2112

Alfa AF: 0.448 Hom.: 26380

Bravo AF: 0.383

Asia WGS AF: 0.436 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.46
PhyloP100		0.58
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: rs4848944; hg19: chr2-125347357;