rs6755697

Variant names:

• chr2-124279347-G-T
• rs6755697
• NM_001367498.1:c.381+36954G>T

Variant summary

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

The NM_001367498.1(CNTNAP5):​c.381+36954G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0462 in 152,004 control chromosomes in the GnomAD database, including 256 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 0.046 (256 hom., cov: 32)
• Consequence: CNTNAP5 NM_001367498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTNAP5	NM_001367498.1	c.381+36954G>T		intron_variant	Intron 3 of 23	ENST00000682447.1	NP_001354427.1
CNTNAP5	NM_130773.4	c.381+36954G>T		intron_variant	Intron 3 of 23		NP_570129.1
CNTNAP5	XM_017003316.2	c.381+36954G>T		intron_variant	Intron 3 of 22		XP_016858805.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTNAP5	ENST00000682447.1	c.381+36954G>T		intron_variant	Intron 3 of 23		NM_001367498.1	ENSP00000508115.1
CNTNAP5	ENST00000431078.1	c.381+36954G>T		intron_variant	Intron 3 of 23	1		ENSP00000399013.1

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7026 AN: 151886 Hom.: 257 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0414

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0403

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0462 AC: 7026 AN: 152004 Hom.: 256 Cov.: 32 AF XY: 0.0472 AC XY: 3507 AN XY: 74318

Gnomad4 AFR AF: 0.0424

Gnomad4 AMR AF: 0.0412

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.0855

Gnomad4 FIN AF: 0.0265

Gnomad4 NFE AF: 0.0403

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.0408 Hom.: 147

Bravo AF: 0.0478

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6755697; hg19: chr2-125036924;