chr2-124225479-T-C

Position:

• chr2-124225479-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367498.1(CNTNAP5):​c.187+3670T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,118 control chromosomes in the GnomAD database, including 47,039 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 0.78 (47039 hom., cov: 33)
• Consequence: CNTNAP5 NM_001367498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNTNAP5	NM_001367498.1	c.187+3670T>C		intron_variant		ENST00000682447.1	NP_001354427.1
CNTNAP5	NM_130773.4	c.187+3670T>C		intron_variant			NP_570129.1
CNTNAP5	XM_017003316.2	c.187+3670T>C		intron_variant			XP_016858805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNTNAP5	ENST00000682447.1	c.187+3670T>C		intron_variant			NM_001367498.1	ENSP00000508115	A1
CNTNAP5	ENST00000431078.1	c.187+3670T>C		intron_variant		1		ENSP00000399013	P4
CNTNAP5	ENST00000470921.1	n.105+3670T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119229 AN: 152000 Hom.: 47005 Cov.: 33

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.784 AC: 119319 AN: 152118 Hom.: 47039 Cov.: 33 AF XY: 0.790 AC XY: 58718 AN XY: 74354

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.777

Alfa AF: 0.789 Hom.: 20607

Bravo AF: 0.782

Asia WGS AF: 0.954 AC: 3319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs1170612; hg19: chr2-124983056;