2-124043657-G-T

Variant names:

• chr2-124043657-G-T
• rs12711664
• NM_001367498.1:c.82+17925G>T

Variant summary

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

The NM_001367498.1(CNTNAP5):​c.82+17925G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 151,998 control chromosomes in the GnomAD database, including 34,281 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 0.67 (34281 hom., cov: 32)
• Consequence: CNTNAP5 NM_001367498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTNAP5	NM_001367498.1	c.82+17925G>T		intron_variant	Intron 1 of 23	ENST00000682447.1	NP_001354427.1
CNTNAP5	NM_130773.4	c.82+17925G>T		intron_variant	Intron 1 of 23		NP_570129.1
CNTNAP5	XM_017003316.2	c.82+17925G>T		intron_variant	Intron 1 of 22		XP_016858805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTNAP5	ENST00000682447.1	c.82+17925G>T		intron_variant	Intron 1 of 23		NM_001367498.1	ENSP00000508115.1
CNTNAP5	ENST00000431078.1	c.82+17925G>T		intron_variant	Intron 1 of 23	1		ENSP00000399013.1
CNTNAP5	ENST00000423939.2	n.446+17925G>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101909 AN: 151884 Hom.: 34251 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.671 AC: 101989 AN: 151998 Hom.: 34281 Cov.: 32 AF XY: 0.674 AC XY: 50039 AN XY: 74278

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.684

Alfa AF: 0.652 Hom.: 23472

Bravo AF: 0.680

Asia WGS AF: 0.637 AC: 2213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
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: rs12711664; hg19: chr2-124801234;