13-57641142-G-C

Variant names:

• chr13-57641142-G-C
• rs9527676
• NM_001040429.3:c.2565+6031G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001040429.3(PCDH17):​c.2565+6031G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: PCDH17 NM_001040429.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

Genes affected

PCDH17 (HGNC:14267): (protocadherin 17) This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein contains six extracellular cadherin domains, a transmembrane domain, and a cytoplasmic tail differing from those of the classical cadherins. The encoded protein may play a role in the establishment and function of specific cell-cell connections in the brain. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH17	NM_001040429.3	c.2565+6031G>C		intron_variant	Intron 1 of 3	ENST00000377918.8	NP_001035519.1
PCDH17	XM_005266357.3	c.2565+6031G>C		intron_variant	Intron 2 of 4		XP_005266414.1
PCDH17	XM_047430276.1	c.2565+6031G>C		intron_variant	Intron 2 of 4		XP_047286232.1
PCDH17	XM_017020547.2	c.2565+6031G>C		intron_variant	Intron 1 of 3		XP_016876036.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCDH17	ENST00000377918.8	c.2565+6031G>C		intron_variant	Intron 1 of 3	1	NM_001040429.3	ENSP00000367151.3
PCDH17	ENST00000484979.5	n.2565+6031G>C		intron_variant	Intron 1 of 3	1		ENSP00000432899.1
PCDH17	ENST00000612954.4	c.729+6031G>C		intron_variant	Intron 1 of 3	5		ENSP00000481329.1
PCDH17	ENST00000615375.1	c.99+6031G>C		intron_variant	Intron 1 of 4	4		ENSP00000483215.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	6.0
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: rs9527676; hg19: chr13-58215276;