rs3805941

Variant names:

• chr6-43089843-A-G
• rs3805941
• NM_002821.5:c.79+13276A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002821.5(PTK7):​c.79+13276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,982 control chromosomes in the GnomAD database, including 14,929 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 0.44 (14929 hom., cov: 31)
• Consequence: PTK7 NM_002821.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 8 publications found

Genes affected

PTK7 (HGNC:9618): (protein tyrosine kinase 7 (inactive)) This gene encodes a member of the receptor protein tyrosine kinase family of proteins that transduce extracellular signals across the cell membrane. The encoded protein lacks detectable catalytic tyrosine kinase activity, is involved in the Wnt signaling pathway and plays a role in multiple cellular processes including polarity and adhesion. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTK7	NM_002821.5	c.79+13276A>G		intron_variant	Intron 1 of 19	ENST00000230419.9	NP_002812.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTK7	ENST00000230419.9	c.79+13276A>G		intron_variant	Intron 1 of 19	1	NM_002821.5	ENSP00000230419.4

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66098 AN: 151864 Hom.: 14908 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.435 AC: 66161 AN: 151982 Hom.: 14929 Cov.: 31 AF XY: 0.433 AC XY: 32182 AN XY: 74282

African (AFR) AF: 0.562 AC: 23277 AN: 41420

American (AMR) AF: 0.387 AC: 5912 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1078 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1850 AN: 5152

South Asian (SAS) AF: 0.489 AC: 2358 AN: 4820

European-Finnish (FIN) AF: 0.351 AC: 3710 AN: 10564

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26673 AN: 67966

Other (OTH) AF: 0.426 AC: 899 AN: 2108

Alfa AF: 0.412 Hom.: 22169

Bravo AF: 0.444

Asia WGS AF: 0.444 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.61
PhyloP100		0.18
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: rs3805941; hg19: chr6-43057581;